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PubMed2005

hATpin, a family of MITE-like hAT mobile elements conserved in diverse plant species that forms highly stable secondary structures.

We identified a 178 bp mobile DNA element in lettuce with characteristic CGAGC/GCTCG repeats in the subterminal regions. This element has terminal inverted repeats and 8-bp target site duplications typical of the hAT superfamily of class II mobile elements, but its small size and potential to form a single-stranded stable hairpin-like secondary structure suggest that it is related to MITE elements. In silico searches for related elements identified 252 plant sequences with 8-bp target site duplications and sequence similarity in their terminal and subterminal regions. Some of these sequences were predicted to encode transposases and may be autonomous elements; these constituted a separate clade within the phylogram of hAT transposases. We demonstrate that the CGAGC/GCTCG pentamer maximizes the hairpin stability compared to any other pentamer with the same C + G content, and the secondary structures of these elements are more stable than for most MITEs. We named these elements collectively as hATpin elements because of the hAT similarity and their hairpin structures. The nearly complete rice genome sequence and the highly advanced genome annotation allowed us to localize most rice elements and to deduce insertion preferences. hATpin elements are distributed on all chromosomes, but with significant bias for chromosomes 1 and 10 and in regions of moderate gene density. This family of class II mobile elements is found primarily in monocot species, but is also present in dicot species.

Base Sequence↗
PubMedDate not supplied

[Conserved regions of potential ORF1 protein products of mobile elements and retroviral proteins, encoded by the gag gene].

Computer search for homology regions of retroelement ORF1 protein products and retroviral gag-encoded proteins was performed using nucleotide and protein sequences of 113 retrotransposons, conservative domains were found in amino acid sequences encoded by viral gene gag: 22 and 17 amino acid residues in capsid and nucleocapsid proteins, respectively. Similar regions were found in potential protein products of ORF1. Another conservative region was revealed by multiple alignment in amino acid sequences of potential protein products of ORF1 of mobile elements and in p19 matrix protein of some retroviruses; this region is different in mobile elements from different classes, but within each class it shows high similarity. The secondary structure of this region is an alpha-helix.

Amino Acid Sequence↗
PubMed2001

Non-autonomous mobile elements in the crenarchaeon Sulfolobus solfataricus.

The genome of the archaeon Sulfolobus solfataricus P2 contains at least four types of short sequence elements lacking open reading frames which are similar to eukaryal non-autonomous mobile elements. The most- conserved elements SM1 (79-80 bp) and SM2 (183-186 bp), with 95 % sequence identity, are present in 40 and 25 copies, respectively. The less-conserved elements SM3 (127-139 bp) and SM4 (160-168 bp), with 75-97 % identity, occur in 44 and 34 copies, respectively. In total, the 143 SM elements constitute about 0.6 % of the genome. The wide distribution of each class of conserved element throughout the genome, and their precise locations, indicate that they are mobile. Direct evidence arises from the presence of SM1 and SM2 in only a fraction of genomic copies of a given class of insertion element, and within copies of open reading frames that are conserved in sequence. SM1 to SM4 are likely to be mobilized by transposases encoded by insertion elements ISC1048, ISC1217, ISC1058 and ISC1173, respectively. Furthermore, the occurrence of clusters of interwoven SM and insertion elements, in potentially mobile units, suggests a mechanism for the transfer of SM elements to other organisms.

Amino Acid Sequence↗
PubMed1984

Complete nucleotide sequence of an unusual mobile element from trypanosoma brucei.

The complete nucleotide sequence of a mobile element from Trypanosoma brucei is presented along with the sequence of its target site, which shows that the insertion has generated a 7 base pair direct repeat. The cloned copy of the element is a dimeric structure, one end of each monomer consisting of a stretch of 14 A residues preceded by a putative trypanosome polyadenylation signal. Six base pairs of DNA of unknown origin are found in the dimer between the two copies of the element. Evidence suggests that the element is present in the genome mainly as a monomer whose sequence is conserved across several species of trypanosome. The element contains an open reading frame encoding the same 160 amino acid protein in both sequenced copies and is extensively transcribed from both strands.

Animals↗
PubMedDate not supplied

[The recombination mechanism for precise excision of the IS50 mobile element in Escherichia coli K12 cells].

Precise excision of composite transposons of Tn10 type, with long inverted repeats, proceeds according to the slippage mechanism (Brunier et al. parallel Cell. 1988. V. 52. P. 883). An alternative recombinational mechanism proved to be possible for transposons with directly oriented IS elements (Goryshin et al. parallel Mol. Biol. 1991. V. 25. P. 614). Making use of an experimental system with plasmid localization of the Tn5 transposon or its IS50 module, we have shown that the recombination mechanism of precise excision can be realized for these mobile elements. The recombination occurs in-trans between direct short repeats flanking a transposon. Formation of a specialized dimer of the original plasmid takes place in this case. The recombination does not depend on the integrity of RecA protein or transposase. Integration of an ori of replication into the mobile element results in the domination of recombination mechanism of precise excision even if the transposon has long inverted repeats at its ends. This seems to occur as a result of inhibition of the slippage mechanism.

Base Sequence↗
PubMed1995

Identification in the human genome of mobile elements spread by DNA-mediated transposition.

We have identified in the human genome two families of mobile elements possessing the sequence characteristics of transposons that move directly from DNA to DNA rather than requiring the reverse transcription of an RNA intermediate. One type of element is closely related to the autonomous transposable element, mariner, and comprises a coding region for a transposase protein flanked by short terminal inverted repeat sequences (TIRs) of 31 or 32 bp. Elements of the second type form a family of short interspersed repetitive elements (SINEs) that are composed simply of two 37 bp TIRs surrounding six unique bps. The TIRs of the human mariner family are identical in all but one position to those of the SINE family, suggesting that the inverted-repeat SINEs represent non-autonomous transposable elements dependent on mariner-type transposase for mobility. Evidence for the mobility of both types of element is provided by examples of their integration into other repeat sequences and by the comparison of orthologous sites in cattle and human genomes. This evidence also shows that these elements have been active in DNA-mediated transposition at some point in the mammalian lineage. Therefore, it appears that the process of DNA-mediated transposition has occurred in mammalian cells and that its maximal cis-requirements are contained in the 80 bp consensus sequence of the human inverted-repeat SINE family.

Amino Acid Sequence↗
PubMedDate not supplied

Prediction of trace element mobility in contaminated soils by sequential extraction.

The modified three-step sequential extraction procedure proposed by the Community Bureau of Reference (or Bureau Communautaire de Reference, BCR) was used to predict trace element mobility in soils affected by an accidental spill comprising arsenopyrite- and heavy metal-enriched sludge particles and acid waste waters. The procedure was used to obtain the distribution of both the major (Al, Ca, Fe, Mg, and Mn) and trace elements (As, Bi, Cd, Cu, Pb, Tl, and Zn) in 13 soils of contrasting properties with various levels of contamination and in the sludge itself. The distributions of the major elements enabled us to confirm the main soil fractions solubilized in each of the three steps, and, in turn, to detect the presence of pyritic sludge particles by the high Fe extractability obtained in the third step. Cadmium was identified as being the most mobile of the elements, having the highest extractability in the first step, followed by Zn and Cu, Lead, Tl, Bi, and As were shown to be poorly mobile or nonmobile. In the case of some of the trace elements, the residual fractions decreased at higher levels of contamination, which was attributed to the anthropogenic contributions to the polluted samples. Comparison with soil-plant transfer factors, calculated in plants growing in the affected area, indicated that a relative sequence of trace element mobility was well predicted from data of the first step.

Accidents↗
PubMed2005

Heritable alteration in DNA methylation pattern occurred specifically at mobile elements in rice plants following hydrostatic pressurization.

Intrinsic DNA methylation pattern is an integral component of the epigenetic network in many eukaryotes. Exploring the extent to which DNA methylation patterns can be altered under a specific condition is important for elucidating the biological functions of this epigenetic modification. This is of added significance in plants wherein the newly acquired methylation patterns can be inherited through organismal generations. We report here that DNA methylation patterns of mobile elements but not of cellular genes were specifically altered in rice plants following hydrostatic pressurization. This was evidenced by methylation-sensitive gel-blot analysis, which showed that 10 out of 10 studied low-copy transposons and retrotransposons manifested methylation alteration in at least one of the 8 randomly chosen pressure-treated plants, whereas none of the 16 studied low-copy cellular genes showed any change. Both gel-blotting and genome-wide fingerprinting indicated that the methylation alteration in mobile elements was not accompanied by a general genetic instability. Progeny analysis indicated retention of the altered methylation patterns in most progeny plants, underscoring early occurrence of the alterations, and their faithful epigenetic inheritance.

Cytosine↗
PubMed1991

Cloning and analysis of the mobile element gypsy from D. virilis.

The homologue of the Drosophila melanogaster mobile element gypsy was cloned from the distantly related species D. virilis. It has three ORFs highly homologous to those of the element from D. melanogaster. gypsy from D. virilis appears to be actively transcribed and is capable of transposition. Comparison of the untranslated regions of both elements revealed conserved sequences including those which had previously been demonstrated to be important in transcription regulation. Distribution of gypsy among the different strains of D. virilis and different species within the D. virilis group was analyzed. Possible involvement of horizontal transmission in the process of spreading and evolution of gypsy is discussed.

Animals↗
PubMed2005

A mobile element based phylogeny of Old World monkeys.

SINEs (Short INterspersed Elements) are a class of non-autonomous mobile elements that are <500 bp in length and have no open reading frames. Individual SINE elements are essentially homoplasy free with known ancestral states, making them useful genetic systems for phylogenetic studies. Alu elements are the most successful SINE in primate genomes and have been utilized for resolving primate phylogenetic relationships and human population genetics. However, no Alu based phylogenetic analysis has yet been performed to resolve relationships among Old World monkeys. Using both a computational approach and polymerase chain reaction display methodology, we identified 285 new Alu insertions from sixteen Old World monkey taxa that were informative at various levels of catarrhine phylogeny. We have utilized these elements along with 12 previously reported loci to construct a phylogenetic tree of the selected taxa. Relationships among all major clades are in general agreement with other molecular and morphological data sets but have stronger statistical support.

Alu Elements↗
PubMed1998

Mobile elements and disease.

A substantial fraction of mammalian genomes is composed of mobile elements and their remnants. Recent insertions of LTR-retrotransposons, non-LTR retrotransposons, and non-autonomous retrotransposons have caused disease frequently in mice, but infrequently in humans. Although many of these elements are defective, a number of mammalian non-LTR retrotransposons of the L1 type are capable of autonomous retrotransposition. The mechanism by which they retrotranspose and in turn aide the retrotransposition of non-autonomous elements is being elucidated.

Animals↗
PubMed2006

An active nonautonomous mobile element in Sulfolobus islandicus REN1H1.

In the crenarchaeote Sulfolobus islandicus REN1H1, a mobile element of 321 bp length has been shown to be active. It does not contain terminal inverted repeats and transposes by a replicative mechanism. This newly discovered element has been named SMN1 (for Sulfolobus miniature noninverted repeat transposable element).

Base Sequence↗
PubMed2004

The vicinity of a broken chromosome end affects P element mobilization in Drosophila melanogaster.

Broken chromosome ends are believed to be capped by a terminal protein complex, and can be maintained in Drosophila melanogaster for many generations. We investigated whether the vicinity of a chromosome end affected P element mobilization and the subsequent repair of the resulting DNA lesion. High levels of P element excision were observed when at least 5 kb of DNA was located between the P element and the end of the chromosome, but recovery of chromosomes from which the P element had been excised was greatly reduced when the chromosome end was positioned less than 5 kb away from the original P element insertion site. Moreover, when the P element was mobilized in terminal deficiency ( y (TD )) alleles, excision events were accompanied by deletions of sequences originally located distal to the P element.

Animals↗
PubMed1989

Mobile elements and transposition events in the cut locus of Drosophila melanogaster.

We have cloned from the Oregon R strain of Drosophila melanogaster a 240 kb segment of DNA that contains the cut (ct) locus, and characterized the region for the presence of repetitive elements. Within this region at least five copies of the suffix element were detected, as well as several putatively novel mobile elements. A number of mutations obtained from the unstable ctMR2 strain and its derivatives were mapped within the cut locus. Comparison between parental and daughter strains indicates that frequently two or more independent transposition events involving the cut locus occur simultaneously within a single germ cell, thus providing a molecular basis for the transposition explosion phenomenon.

Alleles↗
PubMed2005

Comparative mitochondrial genomics in zygomycetes: bacteria-like RNase P RNAs, mobile elements and a close source of the group I intron invasion in angiosperms.

To generate data for comparative analyses of zygomycete mitochondrial gene expression, we sequenced mtDNAs of three distantly related zygomycetes, Rhizopus oryzae, Mortierella verticillata and Smittium culisetae. They all contain the standard fungal mitochondrial gene set, plus rnpB, the gene encoding the RNA subunit of the mitochondrial RNase P (mtP-RNA) and rps3, encoding ribosomal protein S3 (the latter lacking in R.oryzae). The mtP-RNAs of R.oryzae and of additional zygomycete relatives have the most eubacteria-like RNA structures among fungi. Precise mapping of the 5' and 3' termini of the R.oryzae and M.verticillata mtP-RNAs confirms their expression and processing at the exact sites predicted by secondary structure modeling. The 3' RNA processing of zygomycete mitochondrial mRNAs, SSU-rRNA and mtP-RNA occurs at the C-rich sequence motifs similar to those identified in fission yeast and basidiomycete mtDNAs. The C-rich motifs are included in the mature transcripts, and are likely generated by exonucleolytic trimming of RNA 3' termini. Zygomycete mtDNAs feature a variety of insertion elements: (i) mtDNAs of R.oryzae and M.verticillata were subject to invasions by double hairpin elements; (ii) genes of all three species contain numerous mobile group I introns, including one that is closest to an intron that invaded angiosperm mtDNAs; and (iii) at least one additional case of a mobile element, characterized by a homing endonuclease insertion between partially duplicated genes [Paquin,B., Laforest,M.J., Forget,L., Roewer,I., Wang,Z., Longcore,J. and Lang,B.F. (1997) Curr. Genet., 31, 380-395]. The combined mtDNA-encoded proteins contain insufficient phylogenetic signal to demonstrate monophyly of zygomycetes.

Bacteria↗
PubMed2004

Detailed analysis of the insertion site of the mobile elements R997, pMERPH, R392, R705 and R391 in E. coli K12.

The IncJ group of mobile elements have not been extensively studied until recently, due to the inability to isolate extrachromosomal DNA from IncJ-strains. Sequence analysis of the prototype IncJ element, R391, revealed it to be a mosaic structure, integrated into the prfC gene in E. coli. Using inverse PCR (iPCR), we localised the other available IncJ elements (R392, R705, R997 and pMERPH) site of insertion to a 17-bp sequence, within the 5' end of prfC at 99.31 min on the E. coli chromosome, and confirmed this for R391. Despite disrupting prfC, the IncJ's encode novel promoter and 5' sequences, restoring function of the disrupted prfC. Sequence analysis of the elements ends revealed that they contain integrase genes, which share extensive homologies among the group, despite being isolated from broad geographic locations. The elements excise from the host chromosome by recombination between their attL and attR sites, with subsequent recombination between the attP sites on the circular forms and the attB sites in the host genomes. The attB site is highly conserved and found in many different bacteria, suggesting a possible broad host range.

Amino Acid Motifs↗
PubMed1981

Chromosomal locations of two DNA segments that flank ribosomal insertion-like sequences in Drosophila: flanking sequences are mobile elements.

We report the chromosomal locations of two repetitive DNA sequences that flank ribosomal insertion-like sequences in Drosophila melanogaster. The chromocentric region of D. melanogaster contains many copies of sequences that are homologous to type 1 ribosomal insertions. These insertion-like elements are interspersed with other DNA segments that we call flanking sequences. Two distinct flanking sequences derived from the same cloned DNA molecule pDmI 101, the HindIII fragments 101E and 101F, were studied. Whole genome Southern blots with DNA from the D. melanogaster stocks Oregon R (P2), gt-1, and gt-X11 showed complex restriction patterns that differed substantially between the three stocks. This and other data show that flanking sequences are members of diverged repetitive sequence families. In situ hybridization to salivary gland chromosomes of gt-1 and gt-X11 showed that both sequences are homologous to the chromocenter and to about 5 to 8 (101E) or 25 to 30(101F) euchromatic sites in each stock. Most, if not all, of these sites differed in gt-1 and gt-X11. Both 101E and 101F are homologous to he chromocenter and very few euchromatic bands in D. simulans, but 101F is homologous to numerous bands in D. mauritiana. We conclude that the flanking sequences represented by 101E and 101F are mobile elements within the genome of Drosophila. These two sequences differ in several structural features from mobile DNA elements previously described in this organism.

Animals↗
PubMed1995

Tn5384, a composite enterococcal mobile element conferring resistance to erythromycin and gentamicin whose ends are directly repeated copies of IS256.

We have identified a 26-kb mobile element from Enterococcus faecalis CH116, designated Tn5384, which confers resistance to erythromycin and to high levels of gentamicin. Tn5384 is a composite element containing three copies of insertion element IS256. Two of the IS256 copies flank the aac6'-aph2" bifunctional aminoglycoside-modifying-enzyme gene in the inverted orientation, forming a structure similar to staphylococcal gentamicin resistance transposon Tn4001. One of the IS256 elements involved in the Tn4001-like structure also forms the left end of Tn5384, the right end of which is a directly repeated insertion of IS256 approximately 23 kb downstream of the leftmost insertion. Insertions of Tn5384 into enterococcal plasmid pLRM1 have been found associated with 8- and 9-bp duplications of the target sequence.

Base Sequence↗