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PubMed2003

SIRE1, an endogenous retrovirus family from Glycine max, is highly homogeneous and evolutionarily young.

SIRE1 is unusual among Ty1-copia retrotransposons in that it has an additional open reading frame with structural features similar to retroviral envelope proteins between pol and the 3' LTR. Here we report the characterization and comparison of eight different SIRE1 elements derived from a soybean genomic library, as well as SIRE1 reverse transcriptases from Glycine soja. The DNA sequences of the eight SIRE1 elements are highly homogeneous and share greater than 95% nucleotide identity. Partial sequences obtained from BAC ends are similarly conserved. Phylogenetic analyses resolve two closely related SIRE1 lineages, and nucleotide changes within and between SIRE1 lineages have occurred to preserve function. Both the gag and the env-like genes are evolving under similar levels of functional constraint. Considerable sequence heterogeneity in the form of short duplications was found within the LTRs and in the region between the envelope-like ORF and the 3' LTR. These duplications are suggestive of slippage by reverse transcriptase during replication. Sequence identity between LTRs of individual insertions suggests that they transposed within the past 70,000 years. Two of 10 SIRE1 insertions examined abut Ty3-gypsy retroelements. Since the soybean genome harbors more than 1,000 SIRE1 insertions, the collective data suggest that SIRE1 has undergone a very recent and robust amplification in soybean.

Amino Acid Sequence↗

PubMed2004

Retrotransposon-gene associations are widespread among D. melanogaster populations.

We have surveyed 18 natural populations of Drosophila melanogaster for the presence of 23 retrotransposon-gene-association alleles (i.e., the presence of an LTR retrotransposon sequence in or within 1,000 bp of a gene) recently identified in the sequenced D. melanogaster genome. The identified associations were detected only in the D. melanogaster populations. The majority (61%) of the identified retrotransposon-gene associations were present only in the sequenced strain in which they were first identified. Thirty percent of the associations were detected in at least one of the natural populations, and 9% of the associations were detected in all of the D. melanogaster populations surveyed. Sequence analysis of an association allele present in all populations indicates that selection is a significant factor in the spread and/or maintenance of at least some of retroelement-gene associations in D. melanogaster.

Alleles↗

PubMed2004

TAHRE, a novel telomeric retrotransposon from Drosophila melanogaster, reveals the origin of Drosophila telomeres.

Drosophila telomeres do not have typical telomerase repeats. Instead, two families of non-LTR retrotransposons, HeT-A and TART, maintain telomere length by occasional transposition to the chromosome ends. Despite the work on Drosophila telomeres, its evolutionary origin remains controversial. Herein we describe a novel telomere-specific retroelement that we name TAHRE (Telomere-Associated and HeT-A-Related Element). The structure of the three telomere-specific elements indicates a common ancestor. These results suggest that preexisting transposable elements were recruited to perform the cellular function of telomere maintenance. A recruitment similar to that of a retrotransposal reverse transcriptase has been suggested as the common origin of telomerases.

Animals↗

PubMed2004

Structure, divergence, and distribution of the CRR centromeric retrotransposon family in rice.

The centromeric retrotransposon (CR) family in the grass species is one of few Ty3-gypsy groups of retroelements that preferentially transpose into highly specialized chromosomal domains. It has been demonstrated in both rice and maize that CRR (CR of rice) and CRM (CR of maize) elements are intermingled with centromeric satellite DNA and are highly concentrated within cytologically defined centromeres. We collected all of the CRR elements from rice chromosomes 1, 4, 8, and 10 that have been sequenced to high quality. Phylogenetic analysis revealed that the CRR elements are structurally diverged into four subfamilies, including two autonomous subfamilies (CRR1 and CRR2) and two nonautonomous subfamilies (noaCRR1 and noaCRR2). The CRR1/CRR2 elements contain all characteristic protein domains required for retrotransposition. In contrast, the noaCRR elements have different structures, containing only a gag or gag-pro domain or no open reading frames. The CRR and noaCRR elements share substantial sequence similarity in regions required for DNA replication and for recognition by integrase during retrotransposition. These data, coupled with the presence of young noaCRR elements in the rice genome and similar chromosomal distribution patterns between noaCRR1 and CRR1/CRR2 elements, suggest that the noaCRR elements were likely mobilized through the retrotransposition machinery from the autonomous CRR elements. Mechanisms of the targeting specificity of the CRR elements, as well as their role in centromere function, are discussed.

Base Sequence↗

PubMed2005

Dispersal and evolution of the Sinorhizobium meliloti group II RmInt1 intron in bacteria that interact with plants.

Group II introns are both self-splicing RNAs and mobile retroelements found in bacterial and archaeal genomes and in organelles of eukaryotes. They are thought to be the ancestors of eukaryote spliceosomal introns and non-long terminal repeat retrotransposons. We show here that RmInt1, a bacterial group II intron first described in the nitrogen-fixing symbiont of alfalfa (Medicago sativa) Sinorhizobium meliloti, is also present in other Sinorhizobium and Rhizobium species. The intron-homing sites in these species are IS elements of the ISRm2011-2 group as in S. meliloti, but ectopic insertion is also observed. We present evidence that these related bacteria have acquired RmInt1 by vertical inheritance from a common ancestor and by independent horizontal transfer events. We also show that RmInt1 is mobile in related taxa of bacteria that interact with plants and tends to evolve toward an inactive form by fragmentation, with loss of the 3' terminus including the intron-encoded protein. Our results provide an overview of the evolution and dispersion of a bacterial group II intron.

Bacteria↗

PubMed1997

Ribonucleoprotein formation by the ORF1 protein of the non-LTR retrotransposon Tx1L in Xenopus oocytes.

The Tx1L elements constitute a family of site-specific non-LTR retrotransposons found in the genome of the frog Xenopus laevis . The elements have two open reading frames (ORFs) with homology to proteins of retroviruses and other retroelements. This study demonstrates an expected activity of one of the element-encoded proteins. The RNA binding properties of ORF1p, the product of the first ORF of Tx1L, were examined after expression from RNA injected into Xenopus oocytes. Using sucrose gradient sedimentation and non-denaturing gel electrophoresis, we show that ORF1p associates with RNA in cytoplasmic ribonucleoprotein (RNP) particles. Discrete RNPs are formed with well-defined mobilities. The ORF1p RNPs are distinct from endogenous RNPs that contain stored oocyte mRNAs and two specific endogenous mRNAs do not become associated with ORF1p. ORF1p appears to be capable of associating with its own mRNA and with other injected RNAs, independent of specific recognition sequences. Although nuclear localization of ORF1p was anticipated, based both on the supposed mechanism of transposition and on the presence of a potential nuclear localization signal, no significant fraction of the protein was found in the oocyte nucleus. Nonetheless, the RNA binding capability of ORF1p is consistent with the proposed model for transposition of non-LTR retrotransposons.

Animals↗

PubMed1999

A sequence immediately upstream of the plus-strand primer is essential for plus-strand DNA synthesis of the Saccharomyces cerevisiae Ty1 retrotransposon.

Priming of plus-strand DNA is a critical step in reverse transcription of retroviruses and retrotransposons. All retroelements use an RNase H-resistant oligoribonucleotide spanning a purine-rich sequence (the polypurine tract or PPT) to prime plus-strand DNA synthesis. Plus-strand DNA synthesis of the yeast Saccharomyces cerevisiae Ty1-H3 retrotransposon is initiated at two sites, PPT1 and PPT2, located at the upstream boundary of the 3'-long terminal repeat and near the middle of the pol gene in the integrase coding region. The two plus-strand primers have the same purine-rich sequence GGGTGGTA. This sequence is not sufficient by itself to generate a plus-strand origin since two identical sequences located upstream of PPT2 in the integrase coding region are not used efficiently as primers for plus-strand DNA synthesis. Thus, other factors must be involved in the formation of a specific plus-strand DNA primer. We show here that mutations upstream of the PPT in a highly conserved T-rich region severely alters plus-strand DNA priming of Ty1. Our results demonstrate the importance of sequences or structural elements upstream of the PPT for initiation of plus-strand DNA synthesis.

Base Sequence↗

PubMed2000

Determination of L1 retrotransposition kinetics in cultured cells.

L1 retrotransposons are autonomous retroelements that are active in the human and mouse genomes. Previously, we developed a cultured cell assay that uses a neomycin phosphotransferase ( neo ) retrotransposition cassette to determine relative retrotransposition frequencies among various L1 elements. Here, we describe a new retrotransposition assay that uses an enhanced green fluorescent protein (EGFP) retrotransposition cassette to determine retrotransposition kinetics in cultured cells. We show that retrotransposition is not detected in cultured cells during the first 48 h post-transfection, but then proceeds at a continuous high rate for at least 16 days. We also determine the relative retrotransposition rates of two similar human L1 retrotransposons, L1(RP)and L1.3. L1(RP)retrotransposed in the EGFP assay at a rate of approximately 0.5% of transfected cells/day, approximately 3-fold higher than the rate measured for L1.3. We conclude that the new assay detects near real time retrotransposition in a single cell and is sufficiently sensitive to differentiate retrotransposition rates among similar L1 elements. The EGFP assay exhibits improved speed and accuracy compared to the previous assay when used to determine relative retrotransposition frequencies. Furthermore, the EGFP cassette has an expanded range of experimental applications.

3' Untranslated Regions↗

PubMed2001

Pyret, a Ty3/Gypsy retrotransposon in Magnaporthe grisea contains an extra domain between the nucleocapsid and protease domains.

A novel Ty3/Gypsy retrotransposon, named Pyret, was identified in the plant pathogenic fungus Magnaporthe grisea (anamorph Pyricularia oryzae). Pyret-related elements were distributed in a wide range of Pyricularia isolates from various gramineous plants. The Pyret element is 7250 bp in length with a 475 bp LTR and one conceptual ORF. The ORF contains seven nonsense mutations in the reading frame, indicating that the Pyret clone is lightly degenerate. Comparative domain analysis among retroelements revealed that Pyret exhibits an extra domain (WCCH domain) beyond the basic components of LTR retrotransposons. The WCCH domain consists of approximately 300 amino acids and is located downstream of the nucleocapsid domain. The WCCH domain is so named because it contains two repeats of a characteristic amino acid sequence, W-X(2)-C-X(4)-C-X(2)-H-X(3)-K. A WCCH motif-like sequence is found in the precoat protein of some geminiviruses, viral RNA-dependent RNA polymerase and also in an Arabidopsis protein of unknown function. Interestingly, detailed sequence analysis of the gag protein revealed that Pyret, as well as some other chromodomain-containing LTR retrotransposons, displays significant sequence homology with members of the gammaretroviruses (MLV-related retroviruses) in the capsid and nucleocapsid domains. This suggests that chromodomain-containing LTR retrotransposons and gammaretroviruses may share a common ancestor with the gag protein.

Amino Acid Motifs↗

PubMed2001

Sequence organization of barley centromeres.

By sequencing, fingerprinting and in situ hybridization of a centromere-specific large insert clone (BAC 7), the sequence organization of centromeric DNA of barley could be elucidated. Within 23 kb, three copies of the Ty3/gypsy-like retroelement cereba were present. Two elements of approximately 7 kb, arranged in tandem, include long terminal repeats (LTRs) (approximately 1 kb) similar to the rice centromeric retrotransposon RIRE 7 and to the cereal centromeric sequence family, the primer binding site, the complete polygene flanked by untranslated regions, as well as a polypurine tract 5' of the downstream LTR. The high density (approximately 200 elements/centromere) and completeness of cereba elements and the absence of internally deleted elements and solo LTRs from the BAC 7 insert represent unique features of the barley centromeres as compared to those of other cereals. Obviously, the conserved cereba elements together with barley-specific G+C-rich satellite sequences constitute the major components of centromeric DNA in this species.

Blotting, Southern↗

PubMed2003

Database for mobile group II introns.

Group II introns are self-splicing RNAs and retroelements found in bacteria and lower eukaryotic organelles. During the past several years, they have been uncovered in surprising numbers in bacteria due to the genome sequencing projects; however, most of the newly sequenced introns are not correctly identified. We have initiated an ongoing web site database for mobile group II introns in order to provide correct information on the introns, particularly in bacteria. Information in the web site includes: (1) introductory information on group II introns; (2) detailed information on subfamilies of intron RNA structures and intron-encoded proteins; (3) a listing of identified introns with correct boundaries, RNA secondary structures and other detailed information; and (4) phylogenetic and evolutionary information. The comparative data should facilitate study of the function, spread and evolution of group II introns. The database can be accessed at http://www.fp.ucalgary.ca/group2introns/.

Databases, Nucleic Acid↗

PubMed2004

Large-scale determination of the methylation status of retrotransposons in different tissues using a methylation tags approach.

A technique for simultaneous determination of the methylation status of numerous loci containing retroelements (REs) is reported. It is based on the observation that methylated and unmethylated areas in the genome are usually extended, and therefore the methylation of particular methyl-sensitive restriction endonuclease recognition sites might reflect the methylation status of DNA regions around them. The method includes dot-blot hybridization of repeat flanking sequences arrayed on a solid support with specifically amplified flanking regions of presumably unmethylated repeats. A multitude of flanking regions of REs adjacent to unmethylated restriction sites are amplified simultaneously, providing a complex hybridization probe. The technique thus allows the determination of the methylation status of restriction sites, which serve as tags of the methylation status of the surrounding regions. The validity of the technique was confirmed by various means, including bisulfite sequencing. The technique was successfully applied to the identification of methylation patterns of the regions surrounding 38 human-specific HERV-K(HML-2) long terminal repeats in cerebellum- and lymph node-derived genomic DNAs. The described technique can be readily adapted to the use of DNA microarray technology.

Binding Sites↗

PubMed2001

The DIRS1 group of retrotransposons.

Only three retrotransposons of the DIRS1 group have previously been described: DIRS1 from the slime mold Dictyostelium discoideum, PAT from the nematode Panagrellus redivivus, and Prt1 from the zygomycetous fungus Phycomyces blakesleeanus. Analyses of the reverse transcriptase sequences encoded by these elements suggest that they are related to the long terminal repeat (LTR) retroelements, such as the Ty3/gypsy retrotransposons and the vertebrate retroviruses. The DIRS1-group elements, however, have several unusual structural features which distinguish them from typical LTR elements: (1) they lack the capacity to encode DDE-type integrases or aspartic proteases; (2) they have open reading frames (ORFs) of unknown function; (3) they integrate without creating duplications of their target sites; and (4) although they are bordered by terminal repeats, these sequences differ from typical LTRs in that they are either inverted repeats or "split" direct repeats. Because of the small number of DIRS1-like elements described, and the unusual structures of these elements, little is known about their evolution, distribution, and replication mechanisms. Here, we report the identification of several new DIRS1-like retrotransposons, including elements from nematodes, sea urchins, fish, and amphibia. We also present evidence for the existence of DIRS1-like sequences in the human genome. In addition, we show that the lack of DDE-type integrase genes from elements of the DIRS1 group is explained by the finding that the previously uncharacterized ORFs of these elements encode proteins related to the site-specific recombinase of bacteriophage lambda. The presence of lambda-recombinase-like genes in DIRS1 elements also accounts for the lack of target-site duplications for these elements and may be related to the unusual structures of their terminal repeats.

Amino Acid Sequence↗

PubMed2001

Structural and phylogenetic analysis of TRAS, telomeric repeat-specific non-LTR retrotransposon families in Lepidopteran insects.

TRAS1 is a non-LTR retrotransposon inserted specifically into the telomeric repeat (TTAGG)(n) in the silkworm, Bombyx mori. To characterize the evolutionary origin of TRAS-like elements, we identified seven TRAS families (TRAS3, TRAS4, TRAS5, TRAS6, TRASY, TRASZ, and TRASW) from B. mori and four elements from two Lepidoptera, Dictyoploca japonica (TRASDJ) and Samia cynthia ricini (TRASSC3, TRASSC4, and TRASSC9). More than 2,000 copies of various Bombyx TRAS elements accumulated within (TTAGG)(n) sequences as unusual but orderly tandem repeats. The 5' and 3' regions were highly conserved within each class of Bombyx TRAS elements without truncation. This suggests that distinct classes of TRAS have been maintained independently by retrotransposition into (TTAGG)(n). The phylogenetic tree of site-specific retroelements showed that nine TRAS families in Lepidoptera constitute a single phylogenetic group that is closely related to the R1 family that inserts specifically into arthropod 28S rDNA. The higher amino acid sequence identity from endonuclease (EN) to reverse transcriptase (RT) domains between TRAS groups (about 37%-70%) than among TRAS elements and R1Bm (about 25%-30%), may reflect the presence of some DNA structure responsible for their target specificity. Sequence comparison from EN to RT domains among non-LTR elements revealed several regions conserved only within TRAS elements. We found a highly conserved region that resembles the Myb-like DNA-binding structure, between the EN and RT domains. These regions may be involved in site-specific integration of TRAS elements into the (TTAGG)(n) telomeric repeats.

Amino Acid Sequence↗

PubMed2002

Genes of the Pseudoviridae (Ty1/copia retrotransposons).

A comprehensive survey of the Pseudoviridae (Ty1/copia) retroelement family was conducted using the GenBank sequence database and completed genome sequences of several model organisms. Plant genomes were the most abundant sources of Pseudoviridae, with the Arabidopsis thaliana genome having 276 distinct elements. A reverse transcriptase amino acid sequence phylogeny indicated that the Pseudoviridae comprises highly divergent members. Coding sequences for a representative subset of elements were analyzed to identify conserved domains and differences that may underlie functional divergence. With the exception of some fungal elements (e.g., Ty1), most Pseudoviridae encode Gag and Pol on a single open reading frame. In addition to the nearly ubiquitous RNA-binding motif of nucleocapsid, three new conserved domains were identified in Gag. pol-encoded aspartic protease was similar to the retroviral enzyme and could be mapped onto the HIV-1 structure. Pol was highly conserved throughout the family. The greatest divergence among Pol sequences was seen in the C-terminus of integrase (IN). We defined a large motif (GKGY) after the IN catalytic domain that is unique to the Pseudoviridae. Additionally, the extreme C-terminus of IN is rich in simple sequence motifs. A distinct lineage of Pseudoviridae in plants have envlike genes. This lineage has undergone a large expansion of Gag characterized by an alpha-helix-rich domain containing coiled-coil motifs. In several elements, this domain is flanked on both sides by RNA-binding domains. We propose that this monophyletic lineage defines a new Pseudoviridae genus, herein referred to as the AGROVIRUS:

Amino Acid Sequence↗

PubMed2002

Retrotransposons and genomic stability in populations of the young allopolyploid species Spartina anglica C.E. Hubbard (Poaceae).

Spartina x townsendii arose during the end of the 19th century in England by hybridization between the indigenous Spartina maritima and the introduced Spartina alterniflora, native to the eastern seaboard of North America. Duplication of the hybrid genome gave rise to Spartina anglica, a vigorous allopolyploid involved in natural and artificial invasions on several continents. This system allows investigation of the early evolutionary changes that accompany stabilization of new allopolyploid species. Because allopolyploidy may be a genomic shock, eliciting retroelement insertional activity, we examined whether retrotransposons present in the parental species have been activated in the genome of S. anglica. For this purpose we used inter-retrotransposon amplified polymorphism (IRAP) and retrotransposons-microsatellite amplified polymorphism (REMAP) markers, which are multilocus PCR-based methods detecting retrotransposon integration events in the genome. IRAP and REMAP allowed the screening of insertional polymorphisms in populations of S. anglica. The populations are composed mainly of one major multilocus genotype, identical to the first-generation hybrid S. x townsendii. Few new integration sites were encountered in the young allopolyploid genome. We also found strict additivity of the parental subgenomes in the allopolyploid. Both these findings indicate that the genome of S. anglica has not undergone extensive changes since its formation. This contrasts with previous results from the literature, which report rapid structural changes in experimentally resynthesized allopolyploids.

DNA, Plant↗

PubMed2002

Sequence variation and genomic amplification of a family of Gypsy-like elements in the oomycete genus Phytophthora.

A family of sequences resembling Gypsy retroelements was identified and shown to be widely distributed throughout the genus Phytophthora, a member of the algallike oomycete fungi. Polymerase chain reaction (PCR) using specific and degenerate primers detected the family in 29 of 37 species tested. DNA hybridization also failed to detect the sequences in the eight species that were negative in PCR. The element appears to have been a major force in the shaping of Phytophthora genomes because its abundance varied drastically from about 10 to more than 10,000 copies per genome within the species containing the element. Family members diverged from each other by single-base changes, insertions, and deletions, with a mean nucleotide divergence of 16.7%. By constructing phylogenies of the elements, lineages were identified that predated speciation events within Phytophthora and subfamilies that had diverged more recently. The element was studied in detail in Phytophthora infestans, in which about 30 copies are dispersed throughout the genome. Phylogenetic comparisons of the reverse transcriptases placed the family within the Ty3/Gypsy group of long terminal repeat (LTR) retrotransposons, with the closest affinities to elements from plants. However, each of 12 family members sequenced contained defects that would render their protein products inactive, including frameshift mutations within reverse transcriptase domains and truncations that appeared to eliminate gag, protease, and terminal repeat sequences.

Animals↗

PubMed1997

Phylogenetic analysis of a retrotransposon with implications for strong evolutionary constraints on reverse transcriptase.

This study examines the evolutionary dynamics of a retrotransposon in a group of parasitoid wasps. A region containing the reverse transcriptase (RT) domain was sequenced for 43 elements from the genomes of nine different wasp species. Phylogenetic analysis of the elements revealed concordance with taxonomic classification of the host species, and the pattern was consistent with that expected for vertical transmission of a multicopy element during differentiation of the species. Twenty-three of the 43 elements had comparable intact open reading frames in the amplified region, and these were used in an analysis of evolutionary constraint on the amino acid sequence. As previously documented for retroelements, closely related elements exhibited nearly equal substitution rates at nonsynonymous and synonymous sites, but relative nonsynonymous substitution rates decreased as increasingly divergent elements were compared. A statistical test indicated that the decrease was not due to saturation of weakly selected sites. The pattern is most likely caused by a "pseudogene effect." Individual elements are not subject to purifying selection, and therefore, synonymous and nonsynonymous substitutions accumulate at equal rates. Comparisons among closely related elements are influenced strongly by this pseudogene evolution, whereas comparisons among distantly related elements reveal selection on the actively replicating lineages connecting the elements. These distant comparisons more accurately reflect the constraints on the amino acid sequence, and the comparisons among elements in this study indicated strong constraints on RT.

Amino Acid Sequence↗