SEARCH · PubMed Health

Results for “retroelements”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 37 records · Page 2Linked to original sources

PubMedDate not supplied

Grasshopper, a long terminal repeat (LTR) retroelement in the phytopathogenic fungus Magnaporthe grisea.

The fungal phytopathogen Magnaporthe grisea parasitizes a wide variety of gramineous hosts. In the course of investigating the genetic relationship between pathogen genotype and host specificity we identified a retroelement that is present in some strains of M. grisea that infect finger millet and goosegrass (members of the plant genus Eleusine). The element, designated grasshopper (grh), is present in multiple copies and dispersed throughout the genome. DNA sequence analysis showed that grasshopper contains 198 base pair direct, long terminal repeats (LTRs) with features characteristic of retroviral and retrotransposon LTRs. Within the element we identified an open reading frame with sequences homologous to the reverse transcriptase, RNaseH, and integrase domains of retroelement pol genes. Comparison of the open reading frame with sequences from other retroelements showed that grh is related to the gypsy family of retrotransposons. Comparisons of the distribution of the grasshopper element with other dispersed repeated DNA sequences in M. grisea indicated that grasshopper was present in a broadly dispersed subgroup of Eleusine pathogens, suggesting that the element was acquired subsequent to the evolution of this host-specific form. We present arguments that the amplification of different retroelements within populations of M. grisea is a consequence of the clonal organization of the fungal populations.

Amino Acid Sequence↗

PubMed2001

The structure and evolution of Penelope in the virilis species group of Drosophila: an ancient lineage of retroelements.

The Penelope element is the key element responsible for mobilization of other transposable elements in the course of hybrid dysgenesis in Drosophila virilis. Penelope has an unusually complex, highly variable organization in all studied species of the virlis group. Thc BRIDGE1 element from the fish Fugu rubripes is homologous to Penelope, and database searches detected additional homologous sequences among Expressed Sequence Tags from the flatworm Schistosoma mansonii and the nematode Ancylostoma caninum. Phylogenetic analysis shows that the reverse transcriptase of the Penelope group does not belong to any of the characterized major retroelement lineages, but apparently represents a novel branch of non-LTR retroelements. Sequence profile analysis results in the prediction that the C-terminal domain of the Penelope polyprotein is an active endonuclease related to intron-encoded endonucleases and the bacterial repair endonuclease UvrC, which could function as an integrase. No retroelements containing a predicted endonuclease of this family have been described previously. Phylogenetic analysis of Penelope copies isolated from several species of the virilis group reveals two subfamilies of Penelope elements, one of which includes full-length copies whose nucleotide sequences are almost identical, whereas the other one consists of highly diverged defective copies. Phylogenetic analysis of Penelope suggests both vertical transmission of the element and probable horizontal transfers. These findings support the notion that Penelope invasions occurred repeatedly in the evolution of the virilis group.

Amino Acid Sequence↗

PubMed2000

Lack of evidence for cospeciation between retroelements and their hosts.

Some literature is available on cospeciation and on reconstructing the phylogenetic relationships of retroelements, but relatively little consideration has been given to whether there is cospeciation between retroelements and their hosts. Here we address this problem in detail. We conclude that there is no significant evidence for cospeciation between retroelements and their hosts. This conclusion was reached by noting that the branching order of the two phylogenies was no more similar than would be expected by chance.

Algorithms↗

PubMed2006

Diversity and evolution of Ty1-copia and Ty3-gypsy retroelements in the non-photosynthetic flowering plants Orobanche and Phelipanche (Orobanchaceae).

We present the first study on the diversity and evolution of Ty1-copia and Ty3-gypsy retroelements in a group of non-photosynthetic flowering plants. To this end partial sequences of the reverse transcriptase (rt) gene were obtained from 20 clones for each retroelement type from seven and six accessions of Orobanche and Phelipanche (Orobanchaceae), respectively. Overall sequence similarity is higher in Ty3-gypsy elements than in Ty1-copia elements in agreement with the results from other angiosperm groups. Higher sequence diversity and stronger phylogenetic structure, especially of Ty1-copia sequences, in Orobanche species compared to Phelipanche species support the previously suggested hypothesis (based on karyological and cytological data) that genomes of Orobanche species are more dynamic than those of Phelipanche species. No evidence was found for intraspecific differences of retroelement diversity nor for differences between pest taxa and their putative wild relatives, e.g., O. crenata and O. owerini. The occurrence of a few sequences from Phelipanche species in clades otherwise comprising sequences from Orobanche species might be due to horizontal gene transfer, but the alternative of vertical transmission cannot be rejected unambiguously.

Chromosome Mapping↗

PubMed2004

Retroelements and the human genome: new perspectives on an old relation.

Retroelements constitute a large portion of our genomes. One class of these elements, the human endogenous retroviruses (HERVs), is comprised of remnants of ancient exogenous retroviruses that have gained access to the germ line. After integration, most proviruses have been the subject of numerous amplifications and have suffered extensive deletions and mutations. Nevertheless, HERV-derived transcripts and proteins have been detected in healthy and diseased human tissues, and HERV-K, the youngest, most conserved family, is able to form virus-like particles. Although it is generally accepted that the integration of retroelements can cause significant harm by disrupting or disregulating essential genes, the role of HERV expression in the etiology of malignancies and autoimmune and neurologic diseases remains controversial. In recent years, striking evidence has accumulated indicating that some proviral sequences and HERV proteins might even serve the needs of the host and are therefore under positive selection. The remarkable progress in the analysis of host genomes has brought to light the significant impact of HERVs and other retroelements on genetic variation, genome evolution, and gene regulation.

Antibodies, Viral↗

PubMed2000

Species-specific alternative splice mimicry at the growth hormone receptor locus revealed by the lineage of retroelements during primate evolution.

In humans, growth hormone receptor (GHR) transcripts exist in two isoforms differing by the retention (GHRfl) or exclusion (GHRd3) of exon 3, whereas in mice GHRfl is solely expressed. This species-specific expression pattern is believed to result from an alternative splice event that, on the basis of conflicting data obtained in humans, has been considered to be tissue-, developmentally, and/or individual-specific. To decipher the molecular basis of this unusual trait, we isolated a 6.8-kilobase fragment spanning exon 3 from individuals expressing GHRfl. Sequence analysis revealed the existence of two 99% identical retroelements flanking this exon. Unexpectedly, individuals expressing GHRd3 displayed a 2.7-kilobase deletion involving exon 3, which most likely results from an ancestral homologous recombination between the two retroelements. The lineage of these retroelements during primate evolution revealed the species specificity of the GHRd3 allele. These findings led us to propose a model underlying the existence of the sole GHRfl allele in most species. Such a retrovirus-mediated alternative splice mimicry, which clears up several as yet unexplained phenomena (i.e. the above-mentioned expression data, the Mendelian inheritance of GHR expression patterns, and the deletion of nonconsecutive exons in growth hormone resistant patients), represents a novel physiological mechanism accounting for protein diversity between and within species.

Alternative Splicing↗

PubMed2001

A novel hybrid open reading frame formed by multiple cellular gene transductions by a plant long terminal repeat retroelement.

The discovery that vertebrate retroviruses could transduce cellular sequences was central to cancer etiology and research. Although not well documented, transduction of cellular sequences by retroelements has been suggested to modify cellular functions. The maize Bs1 transposon was the first non-vertebrate retroelement reported to have transduced a portion of a cellular gene (c-pma). We show that Bs1 has, in addition, transduced portions of at least two more maize cellular genes, namely for 1,3-beta-glucanase (c-bg) and 1,4-beta-xylan endohydrolase (c-xe). We also show that Bs1 has maintained a truncated gag domain with similarity to the magellan gypsy-like long terminal repeat retrotransposon and a region that may correspond to an env-like domain. Our findings suggest that, like oncogenic retroviruses, the three transduced gene fragments and the Bs1 gag domain encode a fusion protein that has the potential to be expressed. We suggest that transduction by retroelements may facilitate the formation of novel hybrid genes in plants.

Amino Acid Sequence↗

PubMed1995

A novel mechanism of self-primed reverse transcription defines a new family of retroelements.

Retroviruses and long terminal repeat (LTR)-containing retrotransposons initiate reverse transcription by using a specific tRNA primer than anneals to the primer-binding site of the retroelement transcript. Sequences from a large number of retroviruses and LTR-containing retrotransposons had indicated that the role of tRNAs in priming reverse transcription is universal among these LTR-containing retroelements. Data presented here strongly support the surprising conclusion that Tf1, a highly active LTR-containing retrotransposon isolated from Schizosaccharomyces pombe, undergoes a novel self-priming process that requires hybridization between the primer-binding site and the first 11 bases of the Tf1 transcript. Single-base mutations in these regions block transposition and reverse transcription, while compensatory mutations that reestablish complementarily rescue both defects. In addition, the sequence of the minus-strand RNA primer of reverse transcription was consistent with its being derived from the 5' end of the Tf1 transcript. Evidence that this mechanism defines a new family of retroelements is presented.

Base Sequence↗

PubMed1997

Genomic signatures: tracing the origin of retroelements at the nucleotide level.

We investigate the nucleotide sequences of 23 retroelements (4 mammalian retroviruses, 1 human, 3 yeast, 2 plant, and 13 invertebrate retrotransposons) in terms of their oligonucleotide composition in order to address the problem of relationship between retrotransposons and retroviruses, and the coadaptation of these retroelements to their host genomes. We have identified by computer analysis over-represented 3-through 6-mers in each sequence. Our results indicate retrotransposons are heterogeneous in contrast to retroviruses, suggesting different modes of evolution by slippage-like mechanisms. Moreover, we have calculated the Observed/Expected number ratio for each of the 256 tetramers and analysed the data using a multivariate approach. The tetramer composition of retroelement sequences appears to be influenced by host genomic factors like methylase activity.

Animals↗

PubMed1994

Capturing of host DNA by a plant retroelement: Bs1 encodes plasma membrane H(+)-ATPase domains.

The recently identified maize retroelement Bs1 encodes domains of the plasma membrane H(+)-ATPase. This is the first example of host DNA captured by a plant retroelement and resembles the acquisition of oncogenes by vertebrate retroviruses. The ability to capture sequences from its host provides plant retroelements with a mechanism to alter gene structure which could be important for evolutionary adaptive change.

Amino Acid Sequence↗

PubMed1995

Boty, a long-terminal-repeat retroelement in the phytopathogenic fungus Botrytis cinerea.

The phytopathogenic fungus Botrytis cinerea can infect an extremely wide range of host plants (tomato, grapevine, strawberry, and flax) without apparent specialization. While studying genetic diversity in this fungus, we found an element which is present in multiple copies and dispersed throughout the genome of some of its isolates. DNA sequence analysis revealed that the element contained direct, long-terminal repeats (LTRs) of 596 bp whose features were characteristic of retroviral and retrotransposon LTRs. Within the element, we identified an open reading frame with sequences homologous to the reverse transcriptase and RNase H domains of retroelement pol genes. We concluded that the element we had identified was a retroelement and named it Boty. By comparing its open reading frame with sequences from other retroelements, we found that Boty is related to the gypsy family of retrotransposons. Boty was present in numerous strains isolated from grapes and tomatoes but not in isolates from lentils. We propose that Boty-containing and Boty-deficient groups represent two lineages in the population of B. cinerea.

Amino Acid Sequence↗

PubMed2004

Periodic explosive expansion of human retroelements associated with the evolution of the hominoid primate.

Five retroelement families, L1 and L2 (long interspersed nuclear element, LINE), Alu and MIR (short interspersed nuclear element, SINE), and LTR (long terminal repeat), comprise almost half of the human genome. This genome-wide analysis on the time-scaled expansion of retroelements sheds light on the chronologically synchronous amplification peaks of each retroelement family in variable heights across human chromosomes. Especially, L1s and LTRs in the highest density on sex chromosomes Xq and Y, respectively, disclose peak activities that are obscured in autosomes. The periods of young L1, Alu, LTR, and old L1 peak activities calibrated based on sequence divergence coincide with the divergence of the three major hominoid divergence as well as early eutherian radiation while the amplification peaks of old MIR and L2 account for the marsupial-placental split. Overall, the peaks of autonomous LINE (young and old L1s and L2s) peaks and non-autonomous SINE (Alus and MIRs) have alternated repeatedly for 150 million years. In addition, a single burst of LTR parallels the Cretaceous-Tertiary (K-T) boundary, an exceptional global event. These findings suggest that the periodic explosive expansions of LINEs and SINEs and an exceptional burst of LTR comprise the genome dynamics underlying the macroevolution of the hominoid primate lineage.

Animals↗

PubMed1995

Retroelements: propagation and adaptation.

Retroelements are genetic entities that exist in both DNA and RNA forms generated by cyclic alternation of transcription and reverse transcription. They have in common a genetic core (the gag-pol core), encoding conserved functions of a structural protein and a replicase. These are supplemented with a variety of cis-acting nucleic acid sequences controlling transcription and reverse transcription. Most retroelements have additional genes with regulatory or adaptive roles, both within the cell and for movement between cells and organisms. These features reflect the variety of mechanisms that have developed to ensure propagation of the elements and their ability to adapt to specific niches in their hosts with which they co-evolve.

Adaptation, Physiological↗

PubMed2003

Purcopia, a Ty1-copia truncated retroelement in the genome of Claviceps purpurea.

Truncated copy of reverse transcriptase of Ty1/copia retroelement (Purcopia) was found as part of the species-specific RAPD 257(540) marker of Claviceps purpurea. A region of 94 bp with 78.9% identity to an unannotated region of the genomic clone of the rice blast fungus Pyricularia grisea (accession no. AQ162050) was found at the 5' end of the pseudogene. Comparison with database sequences revealed that Purcopia is close to the plant retroelements represented by Tto1, Ta1-3 and Bare-1, whereas the other fungal elements of the Ty1/copia type grouped with Hopscotch elements. Restriction patterns obtained by hybridization of the labeled marker to HindIII digested genomic DNA of various C. purpurea isolates contained multiple bands. The banding was individual and did not yield any species- or population-specific fragments or patterns.

Amino Acid Sequence↗

PubMed2006

Nonneutral GC3 and retroelement codon mimicry in Phytophthora.

Phytophthora is a genus entirely comprised of destructive plant pathogens. It belongs to the Stramenopila, a unique branch of eukaryotes, phylogenetically distinct from plants, animals, or fungi. Phytophthora genes show a strong preference for usage of codons ending with G or C (high GC3). The presence of high GC3 in genes can be utilized to differentiate coding regions from noncoding regions in the genome. We found that both selective pressure and mutation bias drive codon bias in Phytophthora. Indicative for selection pressure is the higher GC3 value of highly expressed genes in different Phytophthora species. Lineage specific GC increase of noncoding regions is reminiscent of whole-genome mutation bias, whereas the elevated Phytophthora GC3 is primarily a result of translation efficiency-driven selection. Heterogeneous retrotransposons exist in Phytophthora genomes and many of them vary in their GC content. Interestingly, the most widespread groups of retroelements in Phytophthora show high GC3 and a codon bias that is similar to host genes. Apparently, selection pressure has been exerted on the retroelement's codon usage, and such mimicry of host codon bias might be beneficial for the propagation of retrotransposons.

Base Composition↗

PubMed2000

Duplication and diversification of the apolipoprotein CI (APOCI) genomic segment in association with retroelements.

We have previously shown that several multicopy gene families within the major histocompatibility complex (MHC) arose from a process of segmental duplication. It has also been observed that retroelements play a role in generating diversity within these duplicated segments. The objective of this study was to compare the genomic organization of a gene duplication within another multicopy gene family outside the MHC. Using new continuous genomic sequence encompassing the APOE-CII gene cluster, we show that APOCI and its pseudogene, APOCI', are contained within large duplicated segments which include sequences from the hepatic control region (HCR). Flanking Alu sequences are observed at both ends of the duplicated unit, suggesting a possible role in the integration of these segments. As observed previously within the MHC, the major differences between the segments are the insertion of sequences (approximately 200-1000 bp in length), consisting predominantly of Alu sequences. Ancestral retroelements also contribute to the generation of sequence diversity between the segments, especially within the 3' poly(A) tract of Alu sequences. The exonic and regulatory sequences of the APOCI and HCR loci show limited sequence diversity, with exon 3 being an exception. Finally, the typing of pre- and postduplication Alus from both segments indicates an estimated time of duplication of approximately 37 million years ago (mya), some time prior to the separation of Old and New World monkeys.

Alu Elements↗

PubMed2004

The diversity of retroelements in diploid and allotetraploid Brassica species.

Using universal PCR primers, some 80 fragments of retroelement reverse transcriptase genes were isolated from 16 accessions of the three diploid and three derived allotetraploid species of Brassica in the triangle of U. Sequence analysis showed that the Ty1/copia and LINE-like elements were distinct, while a third clade could be sub-divided into Ty3/gypsy, Athila and virus-like branches, providing evidence that there are multiple sub-lineages within this group normally considered to be gypsy-like elements in plants. The parsimony trees showed no branches correlating with the known genome relationships for the six diploid and allotetraploid Brassica species, probably because members of the element families were present in the common ancestor of the Brassica and, unlike other repetitive sequences, there is no evidence for genome-wide homogenization, although convergent evolution or horizontal transfer cannot be ruled out. Southern hybridization suggested some sub-families were amplified in individual species. The data show that retroelement sequence data do not allow inference of phylogeny, but knowledge of evolution of such abundant sequences assists in exploitation and interpretation of data from other species including models with much smaller genomes and may provide markers.

Blotting, Southern↗

PubMedDate not supplied

[Multiple template switches on LINE-directed reverse transcription: the most probable formation mechanism for the double and triple chimeric retroelements in mammals].

It was shown that the shuffling mechanism for transcribed genome components, which involves a template switch on the RNA reverse transcription using the L1 retroelement enzymatic machinery, is common in mammals. The occurrence frequency of the resulting chimeric retroelements in the genomes of rodents is twice as high as in the DNA of primates. Moreover, we proved that not only single but also double switches may occur in vivo, which result in the fusion of copies of three different transcripts. Many of the identified chimeras are transcribed in mammals.

Animals↗