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 307 records · Page 17Linked to original sources

PubMed2005

Allopolyploidy--a shaping force in the evolution of wheat genomes.

Recent studies have shown that allopolyploidy accelerates genome evolution in wheat in two ways: (1) allopolyploidization triggers rapid genome changes (revolutionary changes) through the instantaneous generation of a variety of cardinal genetic and epigenetic alterations, and (2) the allopolyploid condition facilitates sporadic genomic changes during the life of the species (evolutionary changes) that are not attainable at the diploid level. The revolutionary changes comprise (1) non-random elimination of coding and non-coding DNA sequences, (2) epigenetic changes such as DNA methylation of coding and non-coding DNA leading, among others, to gene silencing, (3) activation of genes and retroelements which in turn alters the expression of adjacent genes. These highly reproducible changes occur in the F1 hybrids or in the first generation(s) of the nascent allopolyploids and were similar to those that occurred twice in nature: first in the formation of allotetraploid wheat (approximately 0.5 million years ago) and second in the formation of hexaploid wheat (approximately 10,000 years ago). Elimination of non-coding sequences from one of the two homoeologous pairs in tetraploids and from two homoeologous pairs in hexaploids, augments the differentiation of homoeologous chromosomes at the polyploid level, thus providing the physical basis for the diploid-like meiotic behavior of allopolyploid wheat. Regulation of gene expression may lead to improved inter-genomic interactions. Gene inactivation brings about rapid diploidization while activation of genes through demethylation or through transcriptional activation of retroelements altering the expression of adjacent genes, leads to novel expression patterns. The evolutionary changes comprise (1) horizontal inter-genomic transfer of chromosome segments between the constituent genomes, (2) production of recombinant genomes through hybridization and introgression between different allopolyploid species or, more seldom, between allopolyploids and diploids, and (3) mutations. These phenomena, emphasizing the plasticity of the genome with regards to both structure and function, might improve the adaptability of the newly formed allopolyploids and facilitate their rapid and successful establishment in nature.

Chromosomes, Plant↗

PubMed2005

DBR1 siRNA inhibition of HIV-1 replication.

BACKGROUND: HIV-1 and all retroviruses are related to retroelements of simpler organisms such as the yeast Ty elements. Recent work has suggested that the yeast retroelement Ty1 replicates via an unexpected RNA lariat intermediate in cDNA synthesis. The putative genomic RNA lariat intermediate is formed by a 2'-5' phosphodiester bond, like that found in pre-mRNA intron lariats and it facilitates the minus-strand template switch during cDNA synthesis. We hypothesized that HIV-1 might also form a genomic RNA lariat and therefore that siRNA-mediated inhibition of expression of the human RNA lariat de-branching enzyme (DBR1) expression would specifically inhibit HIV-1 replication. RESULTS: We designed three short interfering RNA (siRNA) molecules targeting DBR1, which were capable of reducing DBR1 mRNA expression by 80% and did not significantly affect cell viability. We assessed HIV-1 replication in the presence of DBR1 siRNA and found that DBR1 knockdown led to decreases in viral cDNA and protein production. These effects could be reversed by cotransfection of a DBR1 cDNA indicating that the inhibition of HIV-1 replication was a specific effect of DBR1 underexpression. CONCLUSION: These data suggest that DBR1 function may be needed to debranch a putative HIV-1 genomic RNA lariat prior to completion of reverse transcription.

Cell Line↗

PubMed2003

ORF-less and reverse-transcriptase-encoding group II introns in archaebacteria, with a pattern of homing into related group II intron ORFs.

Although group II intron retroelements are prevalent in eubacteria, they have not been identified in archaebacteria in the first 10 genomes sequenced. However, the recently sequenced archael genome of Methanosarcina acetivorans contains 21 group II introns, including 7 introns that do not encode reverse transcriptase ORFs. To our knowledge, these are the first retroelements identified in archaebacteria, and the first ORF-less group II introns in bacteria. Furthermore, the insertion pattern of the introns is highly unusual. The introns appear to insert site-specifically into ORFs of other group II introns, forming nested clusters of up to four introns, but there are no flanking exons that could encode a functional protein after the introns have been spliced out.

Amino Acid Sequence↗

PubMed1999

Molecular paleontology of transposable elements from Arabidopsis thaliana.

We report results of a comprehensive computer-assisted analysis of new transposable elements (TEs) from Arabidopsis thaliana. Our analysis revealed several previously unknown pogo- and En/Spm-like families and two novel superfamilies of DNA transposons, Arnold and Harbinger. One of the En/Spm-like families (Atenspm) was found to be involved in generating satellite arrays in paracentromeric regions. Of the two superfamilies reported, Harbinger is distantly related to bacterial IS5-like insertion elements, and Arnold contains DNA transposons without terminal inverted repeats (TIRs), which were never reported in eukaryotes before. Furthermore, we report a large number of young and diverse copia-like autonomous and nonautonomous retroelements and discuss their potential evolutionary relationship with mammalian retroviruses. The A. thaliana genome harbors copia-like retroelements which encode a putative env-like protein reported previously in the SIRE-1 retrotransposon from soybean. Finally, we demonstrate a nonrandom chromosomal distribution of the most abundant A. thaliana TEs clustered in the first half of chromosome II, which includes the centromeric region. The families of TEs from A. thaliana are relatively young, extremely diverse and much smaller than those from mammalian genomes. We discuss the potential factors determining similarities and differences in the evolution of TEs in mammals and A. thaliana.

Amino Acid Sequence↗

PubMed2000

Evolution of viruses by acquisition of cellular RNA or DNA nucleotide sequences and genes: an introduction.

The origins of virus evolution may be traced to Archeabacteria since Inouye and Inouye (6) discovered a retroelement with a gene for reverse transcriptase in the bacterial genome and in the satellite, multiple copy single stranded DNA (msDNA) in the soil bacterium Myxococcus xanthus. It was possible (8) to define the evolution of retroelements in eukaryotic cells of plants, insects (gypsy retrovirus) and vertebrates. The replication of RNA viruses in eukaryotic cells allowed for the viral RNA genome to integrate a cellular ubiquitin mRNA, as reported for BVDV (24). Another example is the integration of 28S ribosomal RNA into the hemagglutinin gene of an influenza virus. This change in the hemagglutinin gene led to an increased pathogenicity of the influenza virus (25). In contrast to RNA viruses, DNA viruses had evolved by inserting cDNA molecules derived from mRNA transcripts of cellular genes or foreign viral RNA. It is of interest that the virus acquired cellular genes in the genomes of DNA viruses represent genes that code for proteins that inhibit cellular molecular processes related to HLA class I and II molecules. The other acquired genes are cellular genes that code for cytokines that are capable of inhibiting antigen presentation to T cells by antigen presenting cells (APC) by dendritic Langerhans cells. The acquisition of cellular genes by DNA viruses enhances their pathogenicity by inhibiting the hosts' defense systems.

Animals↗

PubMed1997

About the origin of retroviruses and the co-evolution of the gypsy retrovirus with the Drosophila flamenco host gene.

The gypsy element of Drosophila melanogaster is the first retrovirus identified so far in invertebrates. According to phylogenetic data, gypsy belongs to the same group as the Ty3 class of LTR-retrotransposons, which suggests that retroviruses evolved from this kind of retroelements before the radiation of vertebrates. There are other invertebrate retroelements that are also likely to be endogenous retroviruses because they share with gypsy some structural and functional retroviral-like characteristics. Gypsy is controlled by a Drosophila gene called flamenco, the restrictive alleles of which maintain the retrovirus in a repressed state. In permissive strains, functional gypsy elements transpose at high frequency and produce infective particles. Defective gypsy proviruses located in pericentromeric heterochromatin of all strains seem to be very old components of the genome of Drosophila melanogaster, which indicates that gypsy invaded this species, or an ancestor, a long time ago. At that time, Drosophila melanogaster presumably contained permissive alleles of the flamenco gene. One can imagine that the species survived to the increase of genetic load caused by the retroviral invasion because restrictive alleles of flamenco were selected. The characterization of a retrovirus in Drosophila, one of the most advanced model organisms for molecular genetics, provides us with an exceptional clue to study how a species can resist a retroviral invasion.

Animals↗

PubMed1995

Sequence variability within the tobacco retrotransposon Tnt1 population.

Retroviruses consist of populations of different but closely related genomes referred to as quasispecies. A high mutation rate coupled with extremely rapid replication cycles allows these sequences to be highly interconnected in a rapid equilibrium. It is not known if other retroelements can show a similar population structure. We show here that when the tobacco Tnt1 retrotransposon is expressed, its RNA is not a unique sequence but a population of different but closely related sequences. Nevertheless, this highly variable population is not in a rapid equilibrium and could not be considered as a quasispecies. We have thus named the structure presented by Tnt1 RNA quasispecies-like. We show that the expression of Tnt1 in different situations gives rise to different populations of Tnt1 RNA sequences, suggesting an adaptive capacity for this element. The analysis of the variability within the total genomic population of Tnt1 elements shows that mutations frequently occur in important regulatory elements and that defective elements are often produced. We discuss the implications that this population structure could have for Tnt1 regulation and evolution.

Base Sequence↗

PubMed2001

The diversity of retrotransposons in the yeast Cryptococcus neoformans.

We have undertaken an analysis of the retrotransposons in the medically important basidiomycetous fungus Cryptococcus neoformans. Using the data generated by a C. neoformans genome sequencing project at the Stanford Genome Technology Center, 15 distinct families of LTR retrotransposons and several families of non-LTR retrotransposons were identified. Members of at least seven families have transposed recently and are probably still active. For several families, only partial elements could be identified and these are quite diverse in sequence, suggesting that they are ancient components of the C. neoformans genome. Most C. neoformans elements are not closely related to previously identified fungal retrotransposons, suggesting that the diversity of fungal retrotransposons has been only sparsely sampled to date. C. neoformans has fewer distinct retrotransposon families than Candida albicans (37 or more), in particular fewer families represented solely by ancient and inactive elements, but it has considerably more families than either Saccharomyces cerevisiae (five) or Schizosaccharomyces pombe (two). The findings suggest that elimination of retrotransposons is faster in C. neoformans than in C. albicans, but perhaps not as rapid as in S. cerevisiae or Sz. pombe. The identification of the retrotransposons of C. neoformans should assist in the molecular characterization of this important pathogen, and also further our understanding of the role played by retroelements in genome evolution.

Amino Acid Sequence↗

PubMed1995

Expression of VL30 vectors in human cells that are targets for gene therapy.

Novel vectors made from mouse VL30 retrotransposons were tested in cell types that are targets for gene therapy, including normal human cells (skeletal muscle epithelium, bronchial epithelium, mammary epithelium), Epstein-Barr virus-transformed peripheral blood lymphocytes (PBLs), and various tumor cell lines. The long terminal repeat (LTR) transcriptional promoter, derived from the retroelement NVL-3, expressed abundant mRNA containing the bacterial neomycin resistance gene (neo) in all cell types tested. The amounts of neo RNA detected on RNA blots from normal vs. transformed cells were similar, although relatively less RNA was expressed in PBLs than in other cell types. Vector RNA expression in PBLs persisted during six months of continuous culture. Transcription was regulated by fibroblast growth factor (bFGF) and insulin, with the effects of each being cell-type-dependent. Thus, VL30 vectors introduced and expressed transgenes at significant levels in a number of cell types that are of interest for human gene therapy of metabolic and neoplastic diseases.

Cell Transformation, Neoplastic↗

PubMed1999

Cell cycle control of reverse transcriptase activity for the yeast retrotransposon Ty3.

Retroviruses and retrotransposons depend on their host cells to complete their replication cycles. In many cases, the viral step of reverse transcription is blocked when host cells are arrested in their cell cycle and this block is only released when the host cell resumes division. It has previously been shown that a retrotransposon found in Saccharomyces cerevisiae, Ty3, is unable to produce full-length double-stranded DNA, the product of reverse transcription, when the host cells are arrested in G1. In this study we show that, although Ty3 viruslike particles are produced at equivalent levels in arrested and nonarrested cells, the reverse transcriptase enzyme is inactive in arrested cells. The enzyme activity is restored when the arrested cells are permitted to resume cell division. These data suggest that a host factor regulates the activity of Ty3 reverse transcriptase in the cell cycle, which represents a novel cellular control of retroelements.

G1 Phase↗

PubMed2002

Non-cognate template usage and alternative priming by a group II intron-encoded reverse transcriptase.

Group II introns are retroelements that site-specifically insert into DNA through homing. They are also implicated in related phenomena such as ectopic site insertions and precise intron deletions, but little is known about how group II intron reverse transcriptases (RTs) interact with non-cognate substrates. Here we show that wild-type aI2 RT readily reverse transcribes non-cognate RNAs in mitochondrial RNP particles when the aI2 intron structure is misfolded. In two closely related priming mutants, 1degree2(DeltaD5) and 1(+)2(DeltaD5), which contain wild-type RT but a disrupted intron structure, the RT has substantially lost specificity for aI2 RNA and copies multiple RNAs present in the RNP particles, using an alternative priming mechanism. The RT in 1degree2(DeltaD5) RNP particles can also copy exogenous RNAs but unlike the endogenous templates, a complementary primer is required, suggesting that the alternative priming event is specific to RT-RNA interactions formed in vivo. Alternatively primed cDNAs from strains 1degree2(DeltaD5), 1(+)2(DeltaD5) and 1degree2(P714T) (containing the mutation P714T in the RT) do not use homing site DNA as a primer, but appear to utilize a non-complementary DNA primer of approximately ten nucleotides. The alternative priming mechanism and reverse transcription of non-cognate templates has implications for in vivo reverse transcription of non-intronic RNAs, which is expected to occur during intron deletions and other retroprocessing events.

DNA Primers↗

PubMed1995

The anoxic fibroblast response is an early-stage wound healing program.

When fibroblasts experience anoxia, a cellular program is initiated which results in stepwise activation of an endogenous SVL30 retroelement, metabolic adaptation to reliance on glycolysis, protease secretion, and endonuclease induction. This response is reversible and occurs with no reduction in cellular viability. Examination of experimental wounds reveals that this same response is physiologically activated during the early phase of wound healing when near-anoxic conditions prevail and wound debridement predominates. Procathepsin D has been identified as one of three major anoxia-inducible secretory proteins; its secretion is the result of altered routing within the cell, with no apparent change in the amount of the protein synthesized. A delayed cellular contractile response occurs approximately 1 week after fibroblasts experience as little as 16 hr of anoxia; this response appears to contribute to wound contraction.

Animals↗

PubMed1996

The Env-like open reading frame of the baculovirus-integrated retrotransposon TED encodes a retrovirus-like envelope protein.

TED is a 7.5-kbp member of the gypsy family of retrotransposons that was first identified by its integration within the baculovirus DNA genome. This lepidopteran (moth) transposon contains three retrovirus-like genes, including functional gag and pol that yield reverse transcriptase-containing virus-like particles. To identify and characterize the product(s) of the third env-like open reading frame, TED ORF3 was expressed in homologous lepidopteran cells by using a baculovirus vector, vENV. Immunoblots and immunoprecipitations with antiserum raised against a bacterial ORF3-fusion protein detected two ORF3-encoded proteins, p68env and gp75env. On the basis of selective incorporation of [3H]mannose and inhibition of modification by tunicamycin which blocks N-linked glycosylation, gp75env is a glycoprotein derived from core precursor p68env. As predicted by the presence of a transmembrane domain near the carboxyl terminus, both p68env and gp75env were associated with heavy membranes of vENV-infected cells. Thus, TED ORF3 encodes a membrane glycoprotein with properties characteristic of retroviral env proteins. These data are consistent with the hypothesis that TED is an invertebrate retrovirus. Moreover, TED integration within the baculovirus genome provides an example of retroelement-mediated acquisition of host genes that may contribute to virus evolution.

Animals↗

PubMed1996

Sequence analysis of a cDNA containing the gag and prot regions of the soybean retrovirus-like element, SIRE-1.

SIRE-1 is a family of several hundred dispersed copies of a very large DNA element from Glycine max that has features characteristic of retroviruses and retrotransposons. A 2.4 kb SIRE-1-specific fragment was recovered from a soybean cDNA library and sequenced. The sequence contains two ORFs. Theoretical translation of ORF1 produces a gag-prot-like polyprotein containing highly conserved motifs found in retroelement nucleocapsids (CX2CX4HX4C) and aspartic proteases (LDSG). The second ORF is foreshortened. The cDNA also contains nearly 200 bp of a putative 5' LTR just upstream of a tRNA primer-binding site.

Amino Acid Sequence↗

PubMed1996

Retrotransposon BARE-1 is a major, dispersed component of the barley (Hordeum vulgare L.) genome.

The barley BARE-1 is a transcribed, copia-like retroelement with well-conserved functional domains, an active promoter, and a copy number of at least 3 x 10(4). We examined its chromosomal localization by in situ hybridization. The long terminal repeat (LTR) probe displayed a uniform hybridization pattern over the whole of all chromosomes, excepting paracentromeric regions, telomeres, and nucleolar organizer (NOR) regions. The integrase probe showed a similar pattern. The 5'-untranslated leader (UTL) probe, expected to be the most rapidly evolving component, labeled chromosomes in a dispersed and non-uniform manner, concentrated in the distal regions, possibly indicating a targe site preference.

Base Sequence↗

PubMed1995

Skippy, a retrotransposon from the fungal plant pathogen Fusarium oxysporum.

A retrotransposon from the fungal plant pathogen Fusarium oxysporum f. sp. lycopersici has been isolated and characterized. The element, designated skippy (skp) is 7846 bp in length, flanked by identical long terminal repeats (LTR) of 429 bp showing structural features characteristic of retroviral and retrotransposon LTRs. Target-site duplications of 5 bp were found. Two long overlapping open reading frames (ORF) were identified. The first ORF, 2562 bp in length, shows homology to retroviral gag genes. The second ORF, 3888 bp in length, has homology to the protease, reverse transcriptase. RNase H and integrase domains of retroelement pol genes in that order. Sequence comparisons and the order of the predicted proteins from skippy indicate that the element is closely related to the gypsy family of LTR-retrotransposons. The element is present in similar copy numbers in the two races investigated, although RFLP analysis showed differences in banding patterns. The number of LTR sequences present in the genome is higher than the number of copies of complete elements, indicating excision by homologous recombination between LTR sequences.

Amino Acid Sequence↗

PubMed1995

Analysis and chromosomal localization of retrotransposons in sugar beet (Beta vulgaris L.): LINEs and Ty1-copia-like elements as major components of the genome.

DNA sequences of the reverse transcriptase gene of long terminal repeat (LTR) and non-LTR (non-viral) retrotransposons have been isolated and cloned from the genome of sugar beet (Beta vulgaris). Both retrotransposon types are highly amplified in sugar beet and may account for 2-5% of the genome. The BNR1 family, representing the first non-viral retrotransposon reported from a dicotyledonous species, shows homology to the mammalian L1 family of long interspersed repeated sequences (LINEs) and to retrotransposable elements from maize and lily. Sequences of the Tbv family are homologous to the Ty1-copia class of LTR retrotransposons. The BNR1 and Tbv retrotransposon families are characterized by sequence heterogeneity and are probably defective. The deduced peptide sequences were used to investigate the relation to other retroelements from plants, insects and mammals. Fluorescence in situ hybridization was used to investigate the physical distribution and revealed that both retrotransposon families are present on all sugar beet chromosomes and largely excluded from chromosomal regions harbouring the 18S-5.8S-25S rRNA genes. The BNR1 family is organized in discrete clusters, while the Tbv family of Ty1-copia-like retrotransposons shows a more uniform distribution along chromosome arms and is absent from some chromosomal regions. These contrasting distributions emphasize the differences in evolutionary amplification and dispersion mechanisms between the two types of retrotransposons. The in situ results of both elements reflect significant features of a higher order structure of the genome, as it is known for both short interspersed repeated sequences (SINEs) and LINEs in human.

Amino Acid Sequence↗

PubMed1994

Functional analysis of the tobacco Tnt1 retrotransposon.

Retroelements represent by far the largest and most widespread class of mobile genetic elements. Representative of several classes of retrotransposons have been characterized in a broad range of plant species, but only a few of them have been shown to be active. Among these, the tobacco Tnt1 retrotransposon has been isolated after insertion mutagenesis and is one of the very few to be transcriptionally active. Tnt1 expression is strongly regulated in a tissue-specific and developmental manner. Moreover, Tnt1 expression is induced by a range of biotic or abiotic elicitors, which all have in common the ability to induce the plant defense response. Regulatory sequences involved in this elicitor-mediated induction have been located in the LTR U3 region. The link between Tnt1 activation and the plant defense response might represent an example of the involvement of transposable elements in genome restructurations needed in response to environmental fluctuations such as pathogen attacks.

Base Sequence↗