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PubMed2006

Genetic diversity of SIRE-1 retroelements in annual and perennial Glycine species revealed using SSAP.

Sequence Specific Amplification Polymorphisms (SSAP) were used to measure the distribution and structure of SIRE-1 retroelement populations in annual and perennial Glycine species. For SSAP analysis, primers corresponding to a region immediately upstream of the 3'LTR of the soybean retroelement SIRE-1 were chosen. Analysis reveals that SIRE-1 is present throughout the Glycine genus and shows that the annual species have similar SIRE-1 populations whilst the perennial species have much more distinct and diverse populations. The high number of species-specific subgroups suggest that SIRE-1 has been active and evolving independently in each species during the course of Glycine evolution.

Evolution, Molecular↗

PubMed1999

The fortuitous cloning of retroelement-like sequences from wheat and rye as by-products of a specific polymerase chain reaction.

Cloning of by-products of a specific PCR reaction, directed to the Em genes of wheat and rye, has resulted in the identification of ten sequences with homology to the known Tyl-copia-like retroelements WIS 2-1A from wheat and BARE-1 from barley. These sequences were amplified by only one of the primers due to the presence of an inverted repeat. Nine sequences are ca. 740 bp long and contain part of the left LTR, the adjacent primer-binding site and part of the leader sequence, whereas one shorter sequence (535 bp) consists of part of the leader sequence only. The dendrogram, constructed from the multiple sequence alignment, classified the isolated sequences into two narrowly related groups that belong to the WIS-2 family of cereal retroelements.

Base Sequence↗

PubMed1990

Origin and evolution of retroelements based upon their reverse transcriptase sequences.

To study the evolutionary relationship of reverse transcriptase (RT) containing genetic elements, a phylogenetic tree of 82 retroelements from animals, plants, protozoans and bacteria was constructed. The tree was based on seven amino acid domains totalling 178 residues identified in all RTs. We have also identified these seven domains in the RNA-directed RNA polymerases from various plus-strand RNA viruses. The sequence similarity of these RNA polymerases to RT suggests that these two enzymes evolved from a common ancestor, and thus RNA polymerase can be used as an outgroup to root the RT tree. A comparison of the genetic organization of the various RT containing elements and their position on the tree allows several inferences concerning the origin and evolution of these elements. The most probable ancestor of current retroelements was a retrotransposable element with both gag-like and pol-like genes. On one major branch of the tree, organelle and bacterial sequences (e.g. group II introns and bacterial msDNA) appear to have captured the RT sequences from retrotransposons which lack long terminal repeats (LTRs). On the other major branch, acquisition of LTRs gave rise to two distinct groups of LTR retrotransposons and three groups of viruses: retroviruses, hepadnaviruses and caulimoviruses.

Amino Acid Sequence↗

PubMed2006

The distribution of L1 and Alu retroelements in relation to GC content on human sex chromosomes is consistent with the ectopic recombination model.

The distribution of Alu and L1 retroelements in the human genome changes with their age. Active retroelements target AT-rich regions, but their frequency increases in GC- and gene-rich regions of the genome with increasing age of the insertions. Currently there is no consensus on the mechanism generating this pattern. In this paper we test the hypothesis that selection against deleterious deletions caused by ectopic recombination between repeats is the main cause of the inhomogeneous distribution of L1s and Alus, by means of a detailed analysis of the GC distribution of the repeats on the sex chromosomes. We show that (1) unlike on the autosomes and X chromosome, L1s do not accumulate on the Y chromosome in GC-rich regions, whereas Alus accumulate there to a minor extent; (2) on the Y chromosome Alu and L1 densities are positively correlated, unlike the negative correlation on other chromosomes; and (3) in gene-poor regions of chromosome 4 and X, the distribution of Alus and L1s does not shift toward GC-rich regions. In addition, we show that although local GC content of long L1 insertions is lower than average, their selective loss from recombining chromosomes is not the main cause of the enrichment of ancient L1s in GC-rich regions. The results support the hypothesis that ectopic recombination causes the shift of Alu and L1 distributions toward the gene-rich regions of the genome.

Alu Elements↗

PubMed1992

Retroelements in higher plants.

Representatives of several classes of retroelements have been characterized in a broad range of plant species, where they appear at variable and sometimes very high copy numbers. So far, only a very small number of plant elements have been shown to be active, and this activity seems to be restricted to specific situations of 'genomic shock'. Although it is not yet known whether the presence of retroelements is linked to the high level of variability found in plant genomes, it is now clear that retrotransposons are ancient and ubiquitous components of plant genomes, and could play an important role in plant evolution.

Biological Evolution↗

PubMed1998

SIRE-1, a copia/Ty1-like retroelement from soybean, encodes a retroviral envelope-like protein.

The soybean genome hosts a family of several hundred, relatively homogeneous copies of a large, copia/Ty1-like retroelement designated SIRE-1. A copy of this element has been recovered from a Glycine max genomic library. DNA sequence analysis of two SIRE-1 subclones revealed that SIRE-1 contains a long, uninterrupted, ORF between the 3' end of the pol ORF and the 3' long terminal repeat (LTR), a region that harbors the env gene in retroviral genomes. Conceptual translation of this second ORF produces a 70-kDa protein. Computer analyses of the amino acid sequence predicted patterns of transmembrane domains, alpha-helices, and coiled coils strikingly similar to those found in mammalian retroviral envelope proteins. In addition, a 65-residue, proline-rich domain is characterized by a strong amino acid compositional bias virtually identical to that of the 60-amino acid, proline-rich neutralization domain of the feline leukemia virus surface protein. The assignment of SIRE-1 to the copia/Ty1 family was confirmed by comparison of the conceptual translation of its reverse transcriptase-like domain with those of other retroelements. This finding suggests the presence of a proretrovirus in a plant genome and is the strongest evidence to date for the existence of a retrovirus-like genome closely related to copia/Ty1 retrotransposons.

Amino Acid Sequence↗

PubMed1991

Retronphage phi R73: an E. coli phage that contains a retroelement and integrates into a tRNA gene.

Some strains of Escherichia coli contain retroelements (retrons) that encode genes for reverse transcriptase and branched, multicopy, single-stranded DNA (msDNA) linked to RNA. However, the origin of retrons is unknown. A P4-like cryptic prophage was found that contains a retroelement (retron Ec73) for msDNA-Ec73 in an E. coli clinical strain. The entire genome of this prophage, named phi R73, is 12.7 kilobase pairs and is flanked by 29-base pair direct repeats derived from the 3' end of the selenocystyl transfer RNA gene (selC). P2 bacteriophage caused excision of the phi R73 prophage and acted as a helper to package phi R73 DNA into an infectious virion. The newly formed phi R73 closely resembled P4 as a virion and in its lytic growth. Retronphage phi R73 lysogenized a new host strain, reintegrating its genome into the selC gene of the host chromosome and enabling the newly formed lysogens to produce msDNA-Ec73. Hence, retron Ec73 can be transferred intercellularly as part of the genome of a helper-dependent retronphage.

Base Sequence↗

PubMed2025

Endogenous Retroelement Activation is Implicated in Interferon-α Production and Anti-Cyclic Citrullinated Peptide Autoantibody Generation in Early Rheumatoid Arthritis.

OBJECTIVE: Endogenous retroelements (EREs) stimulate type 1 interferon (IFN-I) production but have not been explored as potential interferonogenic triggers in rheumatoid arthritis (RA). We investigated ERE expression in early RA (eRA), a period in which IFN-I levels are increased. METHODS: ERE expression (long terminal repeat [LTR] 5, long interspersed nuclear element 1 [LINE-1], and short interspersed nuclear element [SINE]) in disease-modifying treatment-naïve eRA whole-blood and bulk synovial tissue samples was examined by reverse transcription-polymerase chain reaction and NanoString alongside IFN-α activity. Circulating lymphocyte subsets, including B cell subsets, from patients with eRA and early psoriatic arthritis (ePsA) were flow cytometrically sorted and similarly examined. Existing established RA and osteoarthritis (OA) synovial single-cell sequencing data were reinterrogated to identify repeat elements, and associations were explored. RESULTS: There was significant coexpression of all ERE classes and IFNA in eRA synovial tissue samples (n = 22, P < 0.0001) and significant positive associations between whole-blood LINE-1 expression (n = 56) and circulating IFN-α protein (P = 0.018) and anti-cyclic citrullinated peptide (anti-CCP) titers (P < 0.0001). ERE expression was highest in circulating eRA B cells, particularly naïve B cells compared with ePsA, with possible ERE regulation by SAM and HD Domain Containing Deoxynucleoside Triphosphate Triphosphohydrolase 1 transcription (SAMDH1) implicated and associations with IFNA again observed. Finally, in established RA synovium, LTRs, particularly human endogenous retroviral sequence K (HERVK), were most increased in RA compared with OA, in which, for all synovial subsets (monocytes, B cells, T cells, and fibroblasts), ERE expression associated with increased IFN-I signaling (P < 0.001). CONCLUSION: Peripheral blood and synovial ERE expression is examined for the first time in eRA, highlighting both a potential causal relationship between ERE and IFN-I production and an intriguing association with anti-CCP autoantibodies. This suggests EREs may contribute to RA pathophysiology with implications for future novel therapeutic strategies.

Humans↗

PubMed1995

Athila, a new retroelement from Arabidopsis thaliana.

An analysis of Arabidopsis thaliana heterochromatic regions allowed the identification of a new family of retroelements called Athila. These 10.5 kb elements, representing ca. 0.3% of the genome, present several features of retrotransposons and retroviruses. Athila elements are flanked by 1.5 kb long terminal repeats (LTR) that are themselves bounded by 5 bp perfect inverted repeats. These LTRs start and end with the retroviral consensus 5'TG...CA3' nucleotides. A putative tRNA-binding site and a polypurine tract are found adjacent to the 5' and 3' LTR respectively. The central domain is composed of two long open reading frames (ORFs) of 935 and 694 amino acids. Despite several indications of recent transposition activity, the translation of these ORFs failed to reveal significant homology with proteins associated to retrotransposition. We suggest that the Athila family could result from the transduction and dispersion of a cellular gene by a retrotransposon.

Amino Acid Sequence↗

PubMed1996

DNA regions flanking the major Arabidopsis thaliana satellite are principally enriched in Athila retroelement sequences.

An analysis of Arabidopsis thaliana heterochromatic regions revealed that genomic sequences immediately flanking the major 180 bp satellite are essentially made of middle repetitive sequences and that most of these sequences correspond to defective Athila retroelements. Using YAC and lambda clones, we evaluated the distribution of Athila elements in the Arabidopsis genome and showed that, despite the presence of numerous euchromatic copies, these elements are especially concentrated in or near heterochromatic regions. Sequencing of the various DNA transitions between satellite and Athila repeats provides strong evidence that most of the heterochromatic elements retrotransposed directly into 180 bp satellite clusters.

Arabidopsis↗

PubMed1995

Evolution and biological significance of human retroelements.

Retroelements comprise a substantial portion of the human genome. Their large number and ubiquitous distribution has led scientists to speculate about their evolutionary origin and their biological functions. Human endogenous retroviruses and their retrotransposon relatives represent a reservoir of possibly pathogenic retroviral genes that may be activated spontaneously or by environmental conditions. They can act as insertion mutagens and activate or inactivate cellular genes, or may be involved in chromosome aberrations by recombination of related elements on different chromosomal locations. Retroviral gene products themselves may also be pathogenic and, for example, could be implicated in the development of tumors and autoimmune diseases. On the other hand, endogenous retroviral elements and nonviral retroposons are thought to have played an important role in shaping the genomes of vertebrates by intracellular transposition events and by generating hot spots of recombination. In the course of time, some of these elements have acquired cellular functions, such as, for instance, in the regulation of gene expression. Therefore, the role of human endogenous retroviruses and retroposons in biological processes is currently a subject of great interest.

Animals↗

PubMed1997

The evolution of MHC diversity by segmental duplication and transposition of retroelements.

Sequence analysis of a 237 kb genomic fragment from the central region of the MHC has revealed that the HLA-B and HLA-C genes are contained within duplicated segments peri-B (53 kb) and peri-C (48 kb), respectively, and separated by an intervening sequence (IF) of 30 kb. The peri-B and peri-C segments share at least 90% sequence homology except when interrupted by insertions/deletions including Alu, L1, an endogenous retrovirus, and pseudogenes. The sequences of peri-B, IF, and peri-C were searched for the presence of Alu elements to use as markers of evolution, chromosomal rearrangements, and polymorphism. Of 29 Alu elements, 14 were identified in peri-B, 11 in peri-C, and 4 in IF. The Alu elements in peri-B and peri-C clustered phylogenetically into two clades which were classified as "preduplication" and "postduplication" clades. Four Alu J elements that are shared by peri-B and peri-C and are flanked by homologous sequences in their paralogous locations, respectively, clustered into a "preduplication" clade. By contrast, the majority of Alu elements, which are unique to either peri-B or peri-C, clustered into a postduplication clade together with the Alu consensus subfamily members ranging from platyrrhine-specific (Spqxcg) to catarrhine-specific Alu sequences (Y). The insertion of platyrrhine-specific Alu elements in postduplication locations of peri-B and peri-C implies that these two segments are the products of a duplication which occurred in primates prior to the divergence of the New World primate from the human lineage (35-44 mya). Examination of the paralogous Alu integration sites revealed that 9 of 14 postduplication Alu sequences have produced microsatellites of different length and sequence within the Alu 3'-poly A tail. The present analysis supports the hypothesis that HLA-B and HLA-C genes are products of an extended segmental duplication between 44 and 81 million years ago (mya), and that subsequent diversification of both genomic segments occurred because of the mobility and mutation of retroelements such as Alu repeats.

Amino Acid Sequence↗

PubMed2003

Characterization of reverse transcriptase activity of the L1Tc retroelement from Trypanosoma cruzi.

The recombinant protein RTL1Tc, encoded by the non-LTR (long terminal repeat) retrotransposon L1Tc from Trypanosoma cruzi, has been shown to have reverse transcriptase (RT) activity using poly(rA)/oligo(dT) and poly(rC)/oligo(dG) homopolymers as template/primers. The optimal RT activity was detected at a concentration of 5 mM Mg2+, pH 8 and between 28 and 37% degrees C. Site-directed mutagenesis in the RT catalytic site proved that substitution of aspartic acid 313 for isoleucine (RT D313IL1Tc) practically abolishes the RT activity of the RTL1Tc protein. RT-polymerase chain reaction assays revealed that the RTL1Tc protein has the ability to use both homologous and heterologous RNA templates. Also, it is shown that the RTL1Tc protein is capable of synthesizing complementary DNA molecules by consecutive switching of the oligo molecule, which the protein uses as a template. This template switching may be involved in the retroelement integration process.

Animals↗

PubMed2004

Retroelements and formation of chimeric retrogenes.

It is very likely that formation of new genes is the main pathway of molecular evolution in living organisms. Many such genes are products of preexisting reshuffling of genetic material. In these processes a very important role is played by mutations associated with the activity of transposable elements, mostly retroelements (REs) for higher eukaryotes. The life cycle of REs involves a stage of so-called reverse transcription of their RNA intermediates, i.e. synthesis of complementary DNA on an RNA template. Transcriptionally active sequences of RE origin are referred to as retrogenes. REs create chimeric genes by a variety of mechanisms: new RE insertions, recombinations between RE sequences, formation of functional gene active pseudogenes and template switches during reverse transcription of messenger RNA. The abovementioned events are also able to give rise to new RE families. These mechanisms are reviewed here along with the description of major RE groups.

Animals↗

PubMed2004

DIRS retroelements in arthropods: identification of the recently active TcDirs1 element in the red flour beetle Tribolium castaneum.

Members of the DIRS family of retrotransposons differ from most other known retrotransposons in that they encode a tyrosine recombinase (YR), a type of enzyme frequently involved in site-specific recombination. This enzyme is believed to insert the extrachromosomal DNA intermediate of DIRS element retrotransposition into the host genome. DIRS elements have been found in plants, a slime mold, fungi, and a variety of animals including vertebrates, echinoderms and nematodes. They have a somewhat patchy distribution, however, apparently being absent from a number of model organisms such as Saccharomyces cerevisiae, Arabidopsis thaliana and Drosophila melanogaster. In this report we describe the first DIRS retroelement to be identified in an arthropod. This element, TcDirs1, was found in the red flour beetle Tribolium castaneum (Coleoptera). It is generally similar in sequence and structure to several previously described members of the DIRS group: it is bordered by inverted terminal repeats and it has a similar set of protein-coding domains (Gag, reverse transcriptase/ribonuclease H, and the YR), although these are arranged in a novel fashion. TcDirs1 elements exhibit several features indicative of recent activity, such as intact coding regions, a high level of sequence similarity between distinct elements and polymorphic insertion sites. Given their presence in an experimentally tractable host, these potentially active elements might serve as useful models for the study of DIRS element retrotransposition. An element closely related to TcDirs1 was also detected in sequences from a second arthropod, the honey bee Apis mellifera (Hymenoptera), suggesting that these retrotransposons are long-term residents of arthropod genomes.

Amino Acid Sequence↗

PubMed2006

Identification of transposons, retroelements, and a gene family predominantly expressed in floral tissues in chromosome 3DS of the hexaploid wheat progenitor Aegilops tauschii.

A multigene family expressed during early floral development was identified on the short arm of wheat chromosome 3D in the region of the Ph2 locus, a locus controlling homoeologous chromosome pairing in allohexaploid wheat. Physical, genetic and molecular characterisation of the Wheat Meiosis 1 (WM1) gene family identified seven members that localised within a region of 173-kb. WM1 gene family members were sequenced and they encode mainly type Ia plasma membrane-anchored leucine rich repeat-like receptor proteins. In situ expression profiling suggests the gene family is predominantly expressed in floral tissue. In addition to the WM1 gene family, a number of other genes, gene fragments and pseudogenes were identified. It has been predicted that there is approximately one gene every 19-kb and that this region of the wheat genome contains 23 repetitive elements including BARE-1 and Wis2-1 like sequences. Nearly 50% of the repetitive elements identified were similar to known transposons from the CACTA superfamily. Ty1-copia, Ty3-gypsy and Athila LTR retroelements were also prevalent within the region. The WM1 gene cluster is present on 3DS and on barley 3HS but missing from the A and B genomes of hexaploid wheat. This suggests either recent generation of the cluster or specific deletion of the cluster during wheat polyploidisation. The evolutionary significance of the cluster, its possible roles in disease response or floral and early meiotic development and its location at or near the Ph2 locus are discussed.

DNA Transposable Elements↗

PubMed2005

A eukaryotic gene family related to retroelement integrases.

Proteins encoded by mobile genetic elements occasionally assume cellular roles. Telomerase, for example, is a reverse transcriptase that replicates chromosome ends, and Rag1 is a transposase that mediates immunoglobulin gene rearrangements. In this article, we report cellular genes related to integrases that are not associated with a retrovirus or retrotransposon. These integrases are found in diverse eukaryotes and are evolving under functional constraint. We propose that the cellular integrases have assumed a host role and, like their retroelement counterparts, probably function in DNA metabolism.

Amino Acid Sequence↗

PubMed1999

Promoter activity of the zebrafish bhikhari retroelement requires an intact activin signaling pathway.

We have investigated mesoderm induction in zebrafish employing the zebrafish LTR-retroelement bhikhari (bik). bik elements are transcribed in all early mesendodermal cells. This expression pattern is generated by a promoter located in the U3 region of the LTR. We show that bik is activated through the activin/Vg1 signaling pathway in an immediate early fashion. This activation critically depends on a sequence motif that occurs among others also in the Xenopus Mix2 activin response element (ARE). It has been shown that the Mix2 ARE binds FAST- 1, which complexes with Smad proteins to form a multi-protein complex. We confirm that also the bik ARE can be bound by FAST-1 in vitro. In animal cap experiments we demonstrate that this binding site is required for activin-induced transcriptional activation mediated by FAST and Smad-type proteins.

Activins↗