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At least 847 records · Page 47Linked to original sources
PubMed1999

A novel tripartite structure comprising a mariner-like element and two additional retrotransposons found in the Bombyx mori genome.

A clone of a DNA-mediated mobile element (transposon) corresponding to a mariner-like element (MLE) was obtained by carrying out the polymerase chain reaction with genomic DNA of Bombyx mori using a Hyalophora cecropia MLE sequence as a primer. This clone had a size of about 4.2 kb and, after sequencing, was found to contain an RNA-mediated, shorter retrotransposon named L1Bm, which was in turn integrated with a much longer retrotransposon named BMC1. Thus, the mobile elements made a novel tripartite structure. The BMC1 and L1Bm moieties of the composite structure each contained a 63-bp conserved sequence which was subsequently found to be highly conserved in all BMC1 and L1Bm elements registered so far. We propose that the 63-bp stretch may be a recognition site for a retrotransposition mechanism conducted by a reverse transcriptase and an endonuclease complex. On the basis of this inference, we propose a model that predicts how different types of BMC1 and L1Bm elements are dispersed in the genome. In addition, a phylogenetic tree made from the current and extant BMC1 and L1Bm sequences indicated that these elements can be classified into Subfamilies I and II.

Animals↗
PubMed1999

Comparison between two human endogenous retrovirus (HERV)-rich regions within the major histocompatibility complex.

Sixteen human endogenous retrovirus (HERV) sequences were detected within 656 kb of genomic sequence obtained from the alpha- and beta-block of the class I region of the major histocompatibility complex (MHC). The HERVs were identified and characterized as family members of HERV-16 (11 copies), HERV-L (1 copy), HERV-I (2 copies), HERV-K91 (1 copy), and HARLEQUIN (1 copy) by sequence comparison using CENSOR or Repeat Masker, BLAST searches, and dot plots. The 11 copies of HERV-16 arose as products of duplication of genomic segments containing HLA class I (HLAcI) and PERB11 (MIC) genes inter alia, whereas the other five HERVs arose after duplication probably as a consequence of single insertion events or translocations. HERV-L and HERV-I are located between the duplicated genes PERB11.2 (MICB) and PERB11.1 (MICA), and HLA-B and HLA-C, respectively, whereas HERV-K91 and HARLEQUIN are located telomeric of HLA-C. A highly fragmented copy of HERV-I was also found telomeric of PERB11. 4. Structural analysis of open reading frames (ORFs) revealed the absence of intact coding sequence within the putative gag, pol, and env gene regions of all the HERVs with the exception of HERV-K91, which had two large ORFs within the region of the putative protease and pol genes. In addition, the 5'-LTR of HERV-L contained a 2.5-kb element that was AT-rich and large ORFs with putative amino acid sequences rich in tyrosines and isoleucines. HERV-I, HARLEQUIN, and at least four copies of HERV-16 appear to have been receptors for the insertion of other retrotransposons including Alu elements and fragments of L1 and THE1. Examination of flanking sequences suggests that HERV-I and HERV-L had occurred by insertion into ancient L1 fragments. This study has revealed that the alpha- and beta-block region within the MHC is rich in HERV sequences occurring at a much higher ratio (10 to 1) than normally observed in the human genome. These HERV sequences will therefore enhance further studies on disease associations and differences between human haplotypes and primates and their role in the evolution of class I genes in the MHC.

Amino Acid Sequence↗
PubMed1999

Characterization of repetitive DNA elements in Arabidopsis.

We have applied computational methods to the available database and identified several families of repetitive DNA elements in the Arabidopsis thaliana genome. While some of the elements have features expected of either miniature inverted-repeat transposable elements (MITEs) or retrotransposons, the most abundant class of repetitive elements, the AthE1 family, is structurally related to neither. The AthE1 family members are defined by conserved 5' and 3' sequences, but these terminal sequences do not represent either inverted or direct repeats. AthE1 family members with greater than 98% identity are easily identified on different Arabidopsis chromosomes. Similar to nonautonomous DNA-based transposon families, the AthE1 family contains members in which the conserved terminal domains flank unrelated sequences. The primary utility of characterizing repetitive sequences is in defining, at least in part, the evolutionary architecture of specific Arabidopsis loci. The repetitive elements described here make up approximately 1% of the available Arabidopsis thaliana genomic sequence.

Algorithms↗
PubMed1999

The role of interelement selection in Saccharomyces cerevisiae Ty element evolution.

Retrotransposons are mobile genetic elements that are ubiquitous components of eukaryotic genomes. The evolutionary success of retrotransposons is explained by their ability to replicate faster than the host genomes in which they reside. Elements with higher rates of genomic replication possess a selective advantage over less active elements. Retrotransposon populations, therefore, are shaped largely by selective forces acting at the genomic level between elements. To evaluate rigorously the effects of selective forces acting on retrotransposons, detailed information on the patterns of molecular variation within and between retrotransposon families is needed. The sequencing of the Saccharomyces cerevisiae genome, which includes the entire genomic complement of yeast retrotransposons, provides an unprecedented opportunity to access and analyze such data. In this study, we analyzed in detail the patterns of nucleotide variation within the open reading frames of two parental (Ty1 and Ty2) and one hybrid (Ty1/2) family of yeast retrotransposons. The pattern and distribution of nucleotide changes on the phylogenetic reconstructions of the three families of Ty elements reveal evidence of negative selection on both internal and external branches of the Ty phylogenies. These results indicate that most, if not all, Ty elements examined represent active or recently active retrotransposon lineages. We discuss the relevance of these findings with respect to the coevolutionary dynamic operating between genomic element populations and the host organisms in which they reside.

Databases, Factual↗
PubMed1999

Identification of multiple Gypsy LTR-retrotransposon lineages in vertebrate genomes.

Gypsy LTR-retrotransposons have been identified in the genomes of many organisms, but only a small number of vertebrate examples have been reported to date. Here we show that members of this family are likely to be widespread in many vertebrate classes with the possible exceptions of mammals and birds. Phylogenetic analyses demonstrate that although there are several distinct lineages of vertebrate gypsy LTR-retrotransposons, the majority clusters into one monophyletic clade. Groups of fungal, plant, and insect elements were also observed, suggesting horizontal transfer between phyla may be infrequent. However, in contrast to this, there was little evidence to support sister relationships between elements derived from vertebrate and insect hosts. In fact, the majority of the vertebrate elements appeared to be most closely related to a group of gypsy LTR-retrotransposons present within fungi. This implies either that at least one horizontal transmission between these two phyla has occurred previously or that a gypsy LTR-retrotransposon lineage has been lost from insect taxa.

Animals↗
PubMed1996

Prt1, an unusual retrotransposon-like sequence in the fungus Phycomyces blakesleeanus.

This work reports the isolation and structural characterization of Prt1, a 4.7 kb retrotransposon-like sequence from the filamentous fungus Phycomyces blakesleeanus. Two open reading frames are found within Prt1. The first shows no similarity with known genes. The second encodes peptide stretches similar to the reverse transcriptase and RNaseH domains of the Ty3/gypsy family of LTR-retrotransposons. Prt1 lacks long terminal repeats, having instead short (54 bp) terminal inverted repeats. No target site duplication has been found. A single copy of Prt1 was detected in the genome of P. blakesleeanus. Adjacent to this sole copy of Prt1, a cluster of various short sequence repeats, both direct and inverted, is found. These sequences, which are reminiscent of defective, non-retroviral transposable elements, are also represented in other regions of the P. blakesleeanus genome.

Amino Acid Sequence↗
PubMed1998

Polymorphism of insertion sites of Ty1-copia class retrotransposons and its use for linkage and diversity analysis in pea.

A sample of 15 cultivars and 56 Pisum accessions from the JIC germplasm core collection has been studied using a modification of the SSAP (sequence-specific amplification polymorphisms) technique; the specific primer was designed to correspond to the polypurine tract (PPT) of PDR1, a Ty1-copia group retrotransposon of pea. Most of these SSAP products were shown to be PDR1 derived. The PDR1 SSAP markers are more informative than previously studied AFLP or RFLP markers and are distributed throughout the genome. Their pattern of variation makes them ideal for integrating genetic maps derived from related crosses. Data sets obtained with AFLP and PDR1 SSAP markers were used to construct neighbour-joining trees and for principal component analysis. These data sets give greater resolution than hitherto available for the characterisation of variation within Pisum, showing that the genus has three main groups: P. fulvum, P. abyssinicum and all other Pisum spp. P. abyssinicum is not a subgroup of cultivated P. sativum, as was previously thought, but has probably been domesticated independently. Modern cultivars are shown to form a single group within Pisum as a whole.

Biological Evolution↗
PubMed1999

Phylogeny and transpositional activity of Ty1-copia group retrotransposons in cereal genomes.

The Ty1-copia group retrotransposon populations of barley (Hordeum vulgare) and bread wheat (Triticum aestivum) have been characterised by degenerate PCR and sequence analysis of fragments of the reverse transcriptase genes. The barley population is comprised of a highly heterogeneous set of retrotransposons, together with a collection of sequences that are closely related to the BARE-1 element. Wheat also contains a highly diverse Ty1-copia retrotransposon population, together with a less prominent BARE-1 subgroup. These data have been combined with previously published Gramineae sequences to construct a composite phylogenetic tree for this class of retrotransposons in cereal grasses. The analysis indicates that the ancestral Gramineae genome contained a heterogeneous population of Ty1-copia group retrotransposons, the descendants of which have proliferated to differing degrees in present-day species. Lastly, the level of recent transpositional activity of two Ty1-copia elements has been estimated by measuring their insertional polymorphism within species. Both transposons are highly polymorphic within all species tested. These data suggest that transposition proficiency may be a common and evolutionarily stable feature of the Ty1-copia group retrotransposons of cereal grasses.

Base Sequence↗
PubMed2003

The first non-LTR retrotransposon characterised in the cephalochordate amphioxus, BfCR1, shows similarities to CR1-like elements.

BfCR1 is the first non-long terminal repeat retrotransposon to be characterised in the amphioxus genome. Sequence alignment of the predicted translation product reveals that BfCR1 belongs to the CR1-like retroposon class, a family widely distributed in vertebrate and invertebrate lineages. Structural analysis shows conservation of the specific motifs of the ORF2-CR1 elements: the N-terminal endonuclease, the reverse transcriptase and the C-terminal domains. The BfCR1 element possesses an atypical 3' terminus consisting of the tandem repeat (AAG)6. We gathered evidence supporting the mobility of this element and report an estimated 15 copies of BfCR1, mostly truncated, per haploid genome, a remarkably low number when compared to that of vertebrates. Phylogenetic analysis, including the amphioxus element, seems to indicate that (i) CR1-like retroposons cluster in a monophyletic group and (ii) the CR1-like family was already present in the chordate ancestor. Our data provide further support for the horizontal transmission of CR1-like elements during early vertebrate evolution.

Amino Acid Sequence↗
PubMed2003

Telomerase-independent mechanisms of telomere elongation.

The ends of linear chromosomes must be elongated in a DNA-replication-independent fashion. For chromosome end elongation the majority of eukaryotes use a specialized reverse transcriptase, telomerase, which adds a short, tandemly repeated DNA sequence motif to chromosome ends. Chromosome elongation can also be achieved, however, by mechanisms other than telomerase. Such elongation events have been detected under conditions where telomerase has been inactivated experimentally and in the few organisms that naturally lack telomerase. We will summarize current knowledge on these telomerase-independent elongation mechanisms in yeast and mammalian cells and will discuss in more detail the telomere elongation mechanism by retrotransposons in Drosophila melanogaster.

Animals↗
PubMed2006

L1Tc non-LTR retrotransposons from Trypanosoma cruzi contain a functional viral-like self-cleaving 2A sequence in frame with the active proteins they encode.

A comparative analysis of 40 Trypanosoma cruzi L1Tc elements showed that the 2A self-cleaving sequence described in viruses is present in them. Of these elements, 72% maintain the canonical 2A motif (DxExNPGP). A high percentage has a conserved point mutation within the motif that has not been previously described. In vitro and in vivo expression of reporter polyproteins showed that the L1Tc2A sequence is functional. Mutations within certain L1Tc2A sequences affect the efficiency of the cleavage. The data indicate that the L1Tc2A sequence may be influencing the L1Tc enzymatic machinery determining the composition and level of the translated products. The residues located immediately upstream of the 2A consensus sequence increase the cleaving efficiency and appear to stabilize the relative amount of translated products.

Amino Acid Sequence↗
PubMed2002

Association of different mobile elements to generate novel integrative elements.

Among the more important problems in modern hospitals is the prevalence of bacterial pathogens expressing resistance to multiple antimicrobial agents. The frequency of multiresistance suggests mechanisms by which bacterial species can concentrate and efficiently exchange a variety of resistance determinants. Mechanisms by which this occurs include insertion of transposons within transposons, coalescence through the activity of insertion sequences and the employment of integrons. In some instances, more than one of these mechanisms is involved in creating large multiresistance genetic elements. The association of the elements with transferable elements or transposons may promote rapid dissemination among clinical strains, and create further opportunities for inclusion of additional resistance determinants.

Bacteria↗
PubMed2002

Comparison of SXT and R391, two conjugative integrating elements: definition of a genetic backbone for the mobilization of resistance determinants.

The SXT element (SXT) is becoming an increasingly prevalent vector for the dissemination of antibiotic resistances in Vibrio cholerae. SXT is a member of a larger family of elements, formerly defined as IncJ plasmids, that are self-transmissible by conjugation and integrate site-specifically into the host chromosome. Comparison of the DNA sequences of SXT and R391, an IncJ element from Providencia rettgeri, indicate that these elements consist of a conserved backbone that mediates the regulation, excision/integration and conjugative transfer of the elements. Both elements have insertions into this backbone that either confer the element-specific properties or are of unknown function. Interestingly, the conserved SXT and R391 backbone apparently contains hotspots for insertion of additional DNA sequences. This backbone represents a scaffold for the mobilization of genetic material between a wide range of gram-negative bacteria, allowing for rapid adaptation to changing environments.

Base Sequence↗
PubMed2002

Dictyostelium mobile elements: strategies to amplify in a compact genome.

Dictyostelium discoideum is a eukaryotic microorganism that is attractive for the study of fundamental biological phenomena such as cell-cell communication, formation of multicellularity, cell differentiation and morphogenesis. Large-scale sequencing of the D. discoideum genome has provided new insights into evolutionary strategies evolved by transposable elements (TEs) to settle in compact microbial genomes and to maintain active populations over evolutionary time. The high gene density (about 1 gene/2.6 kb) of the D. discoideum genome leaves limited space for selfish molecular invaders to move and amplify without causing deleterious mutations that eradicate their host. Targeting of transfer RNA (tRNA) gene loci appears to be a generally successful strategy for TEs residing in compact genomes to insert away from coding regions. In D. discoideum, tRNA gene-targeted retrotransposition has evolved independently at least three times by both non-long terminal repeat (LTR) retrotransposons and retrovirus-like LTR retrotransposons. Unlike the nonspecifically inserting D. discoideum TEs, which have a strong tendency to insert into preexisting TE copies and form large and complex clusters near the ends of chromosomes, the tRNA gene-targeted retrotransposons have managed to occupy 75% of the tRNA gene loci spread on chromosome 2 and represent 80% of the TEs recognized on the assembled central 6.5-Mb part of chromosome 2. In this review we update the available information about D. discoideum TEs which emerges both from previous work and current large-scale genome sequencing, with special emphasis on the fact that tRNA genes are principal determinants of retrotransposon insertions into the D. discoideum genome.

Animals↗
PubMed2004

[Patterns on the skin. New aspects of their embryologic and genetic causes].

The concept of cutaneous mosaicism has now been proven by numerous studies. In this way, the idea that all nevi represent mosaics has so far been confirmed. We can distinguish five different patterns of mosaicism in human skin in the form of lines of Blaschko, checkerboard pattern, phylloid pattern, patchy pattern without midline separation, and lateralization. Two different etiological categories are epigenetic and genomic mosaicism. According to present knowledge all epigenetic mosaics are caused by the activity of retrotransposons. In addition to the well-known examples of functional X-chrosomosome mosaicism, the concept of autosomal functional mosaicism, as observed in mice and dogs, has recently been established. Most likely, this mechanism may also explain the exceptional familial occurrence of pigmentary mosaicism in man. Phylloid hypomelanosis and speckled lentiginous nevus syndrome are recently described phenotypes that can be added to the list of lethal mutations surviving by mosaicism. The concept of type 2 segmental manifestation of autosomal dominant skin diseases has recently been confrirmed at the molecular level in a case of Hailey-Hailey disease. The concept of didymosis may explain why two different nevi can occur in spatial and temporal proximity, e.g., cutis tricolor or phacomatosis pigmentovascularis. The mechanism of paradominant inheritance may explain why some nevi that usually occur sporadically may affect, by way of exception, several members of a family. Examples are sebaceous nevus and Becker nevus. In autosomal recessive skin disorders, an event of loss of homozygosity may occur at an early developmental stage, giving rise to healthy skin areas arranged in a nevoid distribution. For example, when dermatologists examine a patient with xeroderma pigmentosum they should pay particular attention to such areas of revertant mosaicism.

Animals↗
PubMed1997

Biosynthetic retrovectoring systems for gene therapy.

Chemical and physical methods of introducing genes into cells (transfection) are being combined with viral transduction as one possible approach toward overcoming the shortcomings of current gene transfer methods. Although several different strategies are being developed worldwide, this article focuses on modification of retroviral vectoring systems. One goal of this work is to combine the safety and ease of transfection methods with the permanency that is presently achieved only by integrating viruses. Work with retrotransposon pseudotypes, synthetic retrovectors, and liposomal delivery of retrovirus vectors is discussed.

Animals↗
PubMed1999

Fukuyama-type congenital muscular dystrophy: the first human disease to be caused by an ancient retrotransposal integration.

Fukuyama-type congenital muscular dystrophy (FCMD), one of the most common autosomal recessive disorders in the Japanese population, is characterized by congenital muscular dystrophy in combination with cortical dysgenesis (micropolygyria). Recently we identified on chromosome 9q31 the gene responsible for FCMD, which encodes a novel 461 amino acid protein that we have termed fukutin. Most FCMD-bearing chromosomes (87%) derive from a single ancestral founder, whose mutation consisted of a 3-kb retrotransposal insertion in the 3' noncoding region of the fukutin gene. Two independent point mutations causing premature termination confirmed that that this gene is responsible for FCMD. FCMD is the first human disease to be caused by an ancient retrotransposal integration. Fukutin contains an amino-terminal signal sequence, which together with results from transfection experiments suggests that it is an extracellular protein. Discovery of the FCMD gene represents an important step toward greater understanding of the pathogenesis of muscular dystrophies and also of normal brain development.

Abnormalities, Multiple↗