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At least 883 records · Page 49Linked to original sources
PubMed2001

Amplification and phylogenetic relationships of a subfamily of blood, a retrotransposable element of Drosophila.

To get a better understanding of the effect of interelement selection on the variation of long terminal repeat retrotransposon families, we have investigated the evolutionary history of blood in the Drosophila melanogaster species complex. We carried out a PCR approach to amplify the 5' untranslated region from blood in the four species of the complex. This procedure revealed two main classes of size variants. Phylogenetic analyses of nucleotide sequences from these variants and blood elements from the Drosophila Genome Projects database show that elements are grouped according to their size, so that they probably correspond to two subfamilies. These two subfamilies arose prior to the split of the complex, and several facts indicate that the expansion of one of them is leading to the competitive exclusion of the other, at least from the euchromatic regions of the genome.

5' Untranslated Regions↗
PubMed2001

Non-LTR retrotransposons encoding a restriction enzyme-like endonuclease in vertebrates.

All autonomous non-long terminal repeat (non-LTR) retrotransposons reported to date in vertebrates encode an apurinic/apyrimidinic endonuclease-like enzyme necessary for target sequence cleavage and subsequent target-primed reverse transcription. We describe here vertebrate non-LTR retrotransposons encoding another type of endonuclease more related to type IIS restriction enzymes. Such retrotransposons have been detected until now only in trypanosomes, nematodes, and arthropods. The retrotransposon Rex6 was identified in the genome of several teleost fish including Xiphophorus maculatus (platyfish), Oryzias latipes (medakafish), Oreochromis niloticus (Nile tilapia), and Fugu rubripes (Japanese pufferfish). Rex6 encodes a reverse transcriptase and a putative restriction enzyme-like endonuclease and is a member of the R4 family of non-LTR retrotransposons containing the Dong and R4 elements found in nematodes and insects. Rex6 was active in many species during teleost evolution and underwent several bursts of retrotransposition (some of them being relatively recent) leading to a high copy number of Rex6 in the genome of numerous fish. Extremely truncated Rex6-related sequences were detected by database screening in reptiles, including the snake Trimeresus flavoviridis and the lizard Anolis carolinensis, but not in sequences from the human genome project, suggesting that this element might have been lost from certain vertebrate lineages.

Amino Acid Sequence↗
PubMed2001

Structural features of the mdg1 lineage of the Ty3/gypsy group of LTR retrotransposons inferred from the phylogenetic analyses of its open reading frames.

The increasing amount of data generated in recent years has opened the way to exhaustive studies of the relationships among different members of the Ty3/gypsy group of LTR retrotransposons, a widespread group of eukaryotic transposable elements. Former research led to the identification of several independent lineages within this group. One of the worse represented of them is that of mdg1, integrated so far only by the Drosophila retrotransposons mdg1 and 412. Our exhaustive database searches indicate the existence of three other Drosophila members of this lineage. Two of them correspond to elements already known, namely, Stalker and blood, but the third one is a new element, which we have called Pilgrim. This element is well represented within the D. melanogaster genome, as revealed by our Southern blot analysis of different strains. The case of Stalker is particularly remarkable, since its phylogenetic relationships clearly point to the mosaic origin of its genome. Finally, our analysis of the evolution of a small ORF preserved within the 5' leader region of these elements indicates different evolutionary rates, presumably as a result of distinct selective constraints.

Amino Acid Sequence↗
PubMed2000

Characteristic sequence pattern in the 5- to 20-bp upstream region of primate Alu elements.

We conducted comprehensive sequence analysis of 5' flanking regions of primate Alu elements. Information contents were computed and frequencies of 1024 pentanucleotides were measured to approximate the location of a characteristic sequence and to specify its pattern(s), which may be involved in the integration of Alu elements into their host genomes. A large number of samples was used, the wide region of the 5' end of Alu elements was analyzed, and comparisons were made among different subfamilies. Through our analyses, "TTTTAAAAA" or "(T)(m)(A)(n)" can be stated as a candidate for the characteristic sequence pattern, which resides around the region 5 to 20 base pairs upstream of the 5' end of Alu elements. This characteristic sequence pattern was more prominent in the sequences of younger Alus, which is a strong indication that the sequence pattern has a role at the time of Alu integration.

Alu Elements↗
PubMed2003

Sequential cloned gene integration in the yeast Kluyveromyces lactis.

Two integrating vectors developed for use in Saccharomyces cerevisiae were successfully employed for cloned gene integration in the yeast Kluyveromyces lactis. A delta-integrating vector carrying the dominant selection marker neo allowed tandem integrations of a CUP1p-lacZ cassette into one or two chromosomal sites. A delta/UB-integrating vector, which contains a reusable selection cassette, enabled multiple rounds of integration and the sequential insertion of stable, dispersed copies of CUP1p-lacZ. Subsequent gene expression was closely correlated with integrated copy number illustrating the promise of this method for metabolic engineering in K. lactis. While both vectors contain an S. cerevisiae delta target sequence, the presence of delta-like elements in K. lactis has not been confirmed. Given the degree of illegitimate recombination in this yeast species, the insertions likely occurred at random locations in the chromosomes.

Chromosomes, Fungal↗
PubMed1997

Improved efficiency and stability of multiple cloned gene insertions at the delta sequences of Saccharomyces cerevisiae.

Two delta-integration vectors were evaluated for the insertion of an inducible expression cassette (the yeast CUP1 promoter fused to the Escherichia coli lacZ structural gene, CUP1p-lacZ) and a bacterial neomycin-resistance gene (neo) into the genome of Saccharomyces cerevisiae via homologous recombination. Cells containing integrations were selected by resistance to the aminoglycoside G418. The first vector was a traditional construct containing only one delta sequence; with this vector, the transformation efficiency and the number of integrations per cell were quite low. The second carried two delta sequences flanking the desired insert, and the unneeded bacterial sequences were removed by restriction-enzyme digestion immediately before transformation. When this double delta vector was employed, the integrated copy number was more than doubled relative to the single delta system and final beta-galactosidase levels exceeded those obtained with the 2 mu-based plasmid. Furthermore, the integrations appeared more stable in long-term sequential culture (both with and without induction of the lacZ gene) than those obtained via the single delta vector.

Genetic Vectors↗
PubMed2002

Nht2, a copia LTR retrotransposon from a conditionally dispensable chromosome in Nectria haematococca.

In the plant pathogenic ascomycete Nectria haematococca mating population (MP) VI, the conditionally dispensable chromosomes are unstable during sexual reproduction. During mapping of such a chromosome, three dispersed repeats were identified. Nht2, one of these repeated elements, is a long terminal repeat (LTR) retrotransposon that is 5.9 kb in length. Its deduced amino acid sequence is homologous to the four enzymatic domains characteristic of copia retrotransposons, but it contains multiple stop codons and probably is no longer able to transpose autonomously. Nht2's LTRs differ at ten positions and the characteristics of these differences resemble the changes induced by repeat-induced point mutation (RIP) in Neurospora crassa. The likelihood that Nectria haematococca MP VI has a RIP-like process, however, is reduced by the fact that a multi-copy transposon cloned from the same ascospore isolate as Nht2 encodes an intact open reading frame. Nht2 is broadly distributed among isolates collected from a variety of host plants. A limited survey of three field isolates suggests that Nht2 is on only one or a few chromosomes in every genome. Nht2's degeneracy and its widespread distribution within the species both suggest that it is an ancient element within N. haematococca MP VI.

Amino Acid Sequence↗
PubMed2002

Repetitive DNA elements in fungi (Mycota): impact on genomic architecture and evolution.

Repetitive DNA elements, microsatellites or simple repeats, minisatellites, mobile elements that transpose at the level of DNA, retrotransposons and various derivatives thereof are ubiquitous constituents of all fungal genomes. Many of these elements, especially the different types of transposon, have been cloned and characterised at the sequence level. Their biological role, however, has not yet been sufficiently elucidated. We are far from understanding the selection mechanisms that tend to conserve repeated DNA at defined loci. There is also little insight into the mechanisms that provide the balance between spreading repetitive elements within genomes and control of their copy number. Depending on the fungal group, this balance can be stabilised at different levels. Asco- and basidiomycetes rarely contain more than 5% repetitive DNA, whereas the phylogenetically older division Zygomycota is characterised by typically more than 30%. The effects of repetitive DNAs on the expression of adjacent genes are only rarely understood and their role for genomic plasticity on an evolutionary time scale is still especially enigmatic. This survey summarises the main characteristics of well studied experimental systems and intends to define important open questions for stimulating future research.

Base Sequence↗
PubMed2003

Identification of Ty1-copia retrotransposons in three ectomycorrhizal basidiomycetes: evolutionary relationships and use as molecular markers.

We amplified by PCR and sequenced 46 partial Ty1- copia reverse transcriptase (RT) sequences from the ectomycorrhizal basidiomycetes Pisolithus and Laccaria bicolor and the host tree Eucalyptus globulus. Phylogenetic analyses indicated that these sequences represent a new class of Ty1- copia RT, characteristic of basidiomycetes but related to plant Ty1- copia retrotransposons. To generate fingerprints of L. bicolor strains, outward facing PCR primers annealing to RTs were designed. This method, which is a modification of the inter-retrotransposon amplified polymorphism (IRAP) analysis, enables the detection of polymorphisms or changes within the insertion sites of Ty1- copia elements in the genome. Using this method, we investigated whether the transposition of Ty1- copia elements was related to the somaclonal variation observed in L. bicolor S238, an inoculant strain used in French Douglas-fir plantations. Data indicated that no differences in the IRAP fingerprints were detected in phenotypic variants of L. bicolor S238. We reported here for the first time the presence of Ty1- copia retrotransposon sequences in basidiomycetes, which resulted in suitable targets for developing new molecular markers.

Amino Acid Sequence↗
PubMed2003

Genetic conservation versus variability in mitochondria: the architecture of the mitochondrial genome in the petite-negative yeast Schizosaccharomyces pombe.

The great amount of molecular information and the many molecular genetic techniques available make Schizosaccharomyces pombe an ideal model eukaryote, complementary to the budding yeast Saccharomyces cerevisiae. In particular, mechanisms involved in mitochiondrial (mt) biogenesis in fission yeast are more similar to higher eukaryotes than to budding yeast. In this review, recent findings on mt morphogenesis, DNA replication and gene expression in this model organism are summarised. A second aspect is the organisation of the mt genome in fission yeast. On the one hand, fission yeast has a strong tendency to maintain mtDNA intact; and, on the other hand, the mt genomes of naturally occurring strains show a great variability. Therefore, the molecular mechanisms behind the susceptibility to mutations in the mtDNA and the mechanisms that promote sequence variations during the evolution of the genome in fission yeast mitochondria are discussed.

DNA Replication↗
PubMed2000

Yeti--a degenerate gypsy-like LTR retrotransposon in the filamentous ascomycete Podospora anserina.

In the filamentous ascomycete Podospora anserina a 6,935-bp retrotransposon, Yeti, has been identified and characterized. It is flanked by a 5-bp target site duplication and contains long terminal repeats (LTRs) 354 bp in length. The LTRs show a high degree of identity to the previously reported repetitive element repa, a sequence suggested to represent a solo-LTR element of an unknown transposon. In the investigated Podospora strains, the number of complete Yeti copies is significantly lower than the number of repa elements, with up to 25 copies. Yeti appears to be inactive: it is highly degenerate and no transcripts of the element have been detected even in Podospora cultures grown under elevated stress conditions. The amino acid sequences deduced from Yeti display significant homology, particularly in the reverse transcriptase region, to those of other fungal retrotransposons, indicating that it is a member of the gypsy family. As suggested by the unusual dinucleotide content, degeneration of Yeti appears to be the result of a molecular mechanism resembling repeat-induced point mutation in Neurospora crassa.

Amino Acid Sequence↗
PubMed2000

A long terminal repeat retrotransposon Cgret from the phytopathogenic fungus Colletotrichum gloeosporioides on cranberry.

A repetitive DNA element cloned from the cranberry fruit rot pathogen Colletotrichum gloeosporioides has been characterized. Sequence data indicate that it is a long terminal repeat (LTR) retrotransposon of 7,916 base pairs. LTR of 544 base pairs occur at either end of an internal region of 6,828 base pairs. This element, designated Cgret (C. gloeosporioides retrotransposon), encodes two putative polypeptides which have high homology to the gag and pol genes of other fungal retrotransposons. The sequence and structure suggest that Cgret is a member of the gypsy group of LTR retrotransposons. The Cgret retrotransposon was present in all of the cranberry isolates of the fungus C. gloeosporioides from New Jersey and Massachusetts, but not in the cranberry isolates from Wisconsin or Chile. Polymorphisms were detected among field isolates of C. gloeosporioides from various hosts, using hybridization probes derived from the LTR and the reverse transcriptase domain of Cgret. The structural integrity of Cgret suggests that it is still a functional retrotransposon and may be used as a molecular marker to study the genetic diversity distribution of this fungal pathogen.

Chile↗
PubMed1996

Rearrangements at a DNA-fingerprint locus in the rice blast fungus.

Populations of the rice blast fungus, Magnaporthe grisea, can be sorted into clonal lineages based on restriction fragment length polymorphisms (RFLPs) detected with the repetitive DNA sequence MGR586. Mechanisms that produce DNA-fingerprint variation among lineages, are not known. In the process of analyzing the meiotic segregation of MGR586 RFLPs we identified a novel polymorphism, called MGR586-P2, in one member of a sister-spore pair from a complete tetrad. Molecular cloning revealed that P2 was generated by a nearby insertion of a novel, long-terminal-repeat (LTR)-containing retrotransposon. Genetic analysis showed that P2 and its progenitor polymorphism (P1) are alleles of a single polymorphic locus termed MGR586-PL (PL). Surprisingly, we found that a strain harboring PL recurrently produced clonal descendants harboring P1, P2 and possibly a third allele designated P3. PL is not located near a telomeric region. Our results show that some DNA-fingerprint loci may be hypervariable and undergo recurrent rearrangements. These findings have implications for interpreting DNA-fingerprint profiles from M. grisea populations.

Ascomycota↗
PubMed1997

cDNA-mediated Ty recombination can take place in the absence of plus-strand cDNA synthesis, but not in the absence of the integrase protein.

Ty elements belong to the family of LTR-containing retrotransposons. Ty RNA is reverse transcribed by Ty-encoded proteins. The cDNA then transposes to new locations in the genome by a process that involves the integrase protein encoded by the element. We have previously shown that the Ty cDNA molecule can participate in recombination events with genomic Tys. In this study we have analyzed the role of the integrase protein in cDNA-mediated Ty recombination. We found that this process involves the integrase protein in a temperature-dependent manner. In addition we have investigated whether double-stranded DNA is the only molecule that can participate in cDNA-mediated Ty recombination. We have shown that mutations in the polypurine tract that abolish plus-strand synthesis do not prevent cDNA-mediated recombination, implying that other types of intermediates from the reverse-transcription process (e.g. single-stranded DNA or a hybrid RNA-cDNA molecule) can participate in cDNA-mediated Ty recombination.

DNA, Complementary↗
PubMed1999

A 'natural' mutation in Saccharomyces cerevisiae strains derived from S288c affects the complex regulatory gene HAP1 (CYP1).

The HAP1 gene encodes a complex transcriptional regulator of many genes involved in electron-transfer reactions and is essential in anaerobic or heme-depleted conditions. We show here that strains derived from S288c carry a defective Ty1 element inserted in the 3' region of the HAP1 ORF. This mutant allele acts as a HAP1 null allele in terms of cytochrome c expression and CYC1 UAS1-dependent transcription, but is able to sustain limited growth in heme-depleted conditions.

Cytochrome c Group↗
PubMed2000

Characterization of novel rad6/ubc2 ubiquitin-conjugating enzyme mutants in yeast.

Null mutations in the RAD6/UBC2 gene encoding an E2 ubiquitin-conjugating enzyme cause deficiencies in DNA repair, N-end-rule protein degradation, sporulation and telomeric silencing, and alter the preferred integration positions for Ty1 retrotransposons. Here we selected for mutants of RAD6 that cause a release of telomeric silencing. Some alleles retained nearly wild-type ability for sporulation, DNA repair and the degradation of proteins. Alteration in Ty1 integration-site bias accompanied some of these alleles. The possibility that some mutations specifically affect binding of an unknown protein that works with Rad6 in its silencing role, but is not required for DNA repair or N-end-rule activity, is discussed in terms of the Rad6 crystal structure.

Alleles↗
PubMed2001

Hideaway, a repeated element from Ascobolus immersus, is rDNA-associated and may resemble a retrotransposon.

A lambda library of Ascobolus immersus stock 50 was screened for repeated DNA sequences by employing differential hybridization to identify transposable elements. Several lambda clones carrying repeated DNA sequences were obtained. One clone contains a repeated DNA sequence with unusual characteristics. This DNA element appears to be associated with rDNA sequences. Its methylation pattern is also reminiscent of rDNA. Sequence analysis indicates that all or at least many copies of the element have integrated in the external spacer sequence separating the rDNA repeats, possibly to avoid complete inactivation by methylation. The element has been named "Hideaway". It possesses structural characteristics of class I retrotransposons, most notably the presence of long direct repeats. The data presented here are discussed with respect to the ability of repeated DNA sequences to escape host defense mechanisms.

Ascomycota↗
PubMed2003

Hypermethylation of retrotransposons in the liverwort Marchantia paleacea var. diptera.

Three DNA fragments encoding part of a reverse transcriptase similar to that of Ty1- copia retrotransposons were isolated from suspension-cultured cells of the liverwort Marchantia paleacea var. diptera. Digestion of total DNA with methylation-sensitive and -insensitive isoschizomers revealed that, like those of the subtelomeric region, CpG sequences in retrotransposon genes were hypermethylated. The methylation status and expression of these retrotransposons was less affected by 5-azadeoxycytidine treatment compared to the subtelomeric region, which was considerably demethylated.

Amino Acid Sequence↗