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At least 469 records · Page 26Linked to original sources

PubMed1999

Differentially expressed transcripts in X-ray-induced lymphomas identified by dioxygenin-labeled differential display.

Differential display is an easily applied method for comparing gene expression in a variety of systems. We used a nonradioactive differential display technique to analyze X-ray-induced lymphomas derived from Emu-pim-1 transgenic and nontransgenic mice. Fragments of 11 differentially regulated genes were identified, three of which are novel sequences. One of the cloned fragments contained sequences of a mouse VL30 retroelement that was significantly overexpressed in a subset of lymphomas as compared with non-lymphomatous tissue. Interestingly, these lymphomas also displayed high levels of c-myc transcripts. An altered expression pattern of a glutathione S-transferase homologue was identified in several lymphomas. Moreover, a cytotoxic T-lymphocyte lipase appeared to be overexpressed specifically in lymphoma-containing spleen tissue, and the results suggest that it may be related to the endogenous immune response against lymphoma development.

Animals↗

PubMed2000

Retrotransposon activation followed by rapid repression in introgressed rice plants.

Plant retrotransposons are largely inactive during normal development, but may be activated by stresses. Both copia-like and gypsy-like retrotransposons of rice were activated by introgression of DNA from the wild species Zizania latifolia Griseb. The copy number increase was associated with cytosine methylation changes of the elements. Activity of the elements was ephemeral, as evidenced by nearly identical genomic Southern hybridization patterns among randomly chosen individuals both within and between generations for a given line, and the absence of transcripts based on Northern analysis. DNA hypermethylation, internal sequence deletion, and possibly other mechanisms are likely responsible for the rapid element repression. Implications of the retroelement dynamics on plant genome evolution are discussed.

Cytosine↗

PubMed2000

Different classes of retrotransposons in coniferous spruce species.

We have used the conservation of reverse transcriptase and integrase domains among retroelements to PCR-amplify three well-known types of these mobile genetic elements. Reverse transcriptase sequences from Ty1-copia were identified in spruce in this way, as well as integrase sequences from the Ty3-gypsy group. Using these sequences as probes against a Picea glauca genomic bank, individual members from the LTR (long terminal direct repeat) groups were obtained. A partial Ty1-copia-type element named Spcl was isolated along with a Ty3-gypsy-type element named Spdl. Genomic Southern hybridizations revealed the complexity and high copy number of LTR retrotransposons in black and white spruce.

Amino Acid Sequence↗

PubMed2002

[Acquisition and loss of modules: the construction set of transposable elements].

Phylogenetic analysis of transposable elements (TEs) allows us to define the relationships between the domains or gene(s) that compose them. Moreover, modules of a few amino-acids can be detected within gag, pol, env genes or within the integrase domain of retrotransposons and transposase of DNA elements. The combination of these observations clearly shows that the evolutionary history of TEs is the outcome of the acquisition and loss of modules with differing origins and histories. This raises the question of the origin of TEs: are they derived from viruses? Are they where viruses come from? Do the basic building bricks come from the prokaryotes, and can they be assembled in the eukaryotes? Are the TEs found in prokaryotes the result of the disintegration of complex elements such as retroelements? Do they evolve from the simplest to the more complex, or are they opportunistic sequences evolving by acquiring and/or losing modules which may be either important or superfluous to their fitness (i.e., their ability to transpose). These are some of the questions that are addressed and discussed in the light of the comparative structures of TEs.

Catalytic Domain↗

PubMed2003

[The unusual mobile element Penelope and its behavior in distant Drosophila species].

The retroelement Penelope isolated from Drosophila virilis has a very unusual structure and codes for reverse transcriptase and an endonuclease belonging to the UvrC type. As shown previously, Penelope is a key element in induction of the hybrid dysgenesis syndrome described in D. virilis, which also involves mobilization of several unrelated mobile element families. Here we report a successful introduction of Penelope into the D. melanogaster genome by P element-mediated transformation. In the new host genome, Penelope is actively transcribed producing major transcript which coincides with that detected in dysgenic hybrids of D. virilis. In situ hybridization on D. melanogaster polytene chromosomes and Southern blotting revealed multiple transpositions of Penelope in the transformed D. melanogaster strains. We determined the structure of six Penelope copies inserted into D. melanogaster chromosomes. Some transformed D. melanogaster strains showed dysgenesis effects similar to those observed in hybrids from D. virilis dysgenic crosses.

Animals↗

PubMedDate not supplied

[Determination of the endonuclease activity encoded by retrotransposon].

Mobile element Penelope is mobilized in the course of hybrid dysgenesis in D. virilis. This element is also responsible for the activation of other unrelated families of TE occurring in the progeny of dysgenic crosses. Penelope elements have extremely variable structure and combine some properties of LINEs and LTR-containing elements. Penelope-like elements (PLEs) have been recently described in various organisms including fish species, rotifers and amoebae. Computer analysis enabled to predict the presence of reverse transcriptase domain in Penelope-encoded polyprotein as well as UvrC type endonuclease at the C-end of the element. It is noteworthy that none of the previously described retroelements was shown to contain such a nuclease. Multiple alignments revealed five conservative catalytic motifs and all conservative residues present in GIY-YIG endonuclease family within Penelope-encoded protein. Herein we have demonstrated that Penelope element isolated from D. virilis encodes functionally active endonuclease exhibiting some sequence-specificity to the sequence previously demonstrated to serve as Penelope genomic insertion site.

Amino Acid Sequence↗

PubMed2005

[Relationship of activation of Tos17 and rice adult plant resistance to bacterial blight].

to investigate whether rice adult plant resistance (APR) is related to activation of long terminal repeat (LTR) retroelements, polymorphism of LTR retroelemnts Tos17 are studied using SSAP (Sequence-Specific Amplification Polymorphism) in seedlings and adult plants of rice cultivar Wase Aikoku 3 inoculated with Xanthomonas oryzae pv. Oryzae, water and those untreated. Of 2000 fragments detected, 9 and 2 are activated in seedlings and adult plants induced by development, respectively; each 3 fragments are activated in seedlings and adult plants induced by pathogen, respectively. The number of activated Tos17 induced by development is more in seedlings than that in adult plants while it is equal due to pathogen induction in seedlings and adult plants, suggest that the activation of Tos17 induced by development probably associate with rice APR to bacterial blight.

Amplified Fragment Length Polymorphism Analysis↗

PubMedDate not supplied

[Conserved regions of potential ORF1 protein products of mobile elements and retroviral proteins, encoded by the gag gene].

Computer search for homology regions of retroelement ORF1 protein products and retroviral gag-encoded proteins was performed using nucleotide and protein sequences of 113 retrotransposons, conservative domains were found in amino acid sequences encoded by viral gene gag: 22 and 17 amino acid residues in capsid and nucleocapsid proteins, respectively. Similar regions were found in potential protein products of ORF1. Another conservative region was revealed by multiple alignment in amino acid sequences of potential protein products of ORF1 of mobile elements and in p19 matrix protein of some retroviruses; this region is different in mobile elements from different classes, but within each class it shows high similarity. The secondary structure of this region is an alpha-helix.

Amino Acid Sequence↗

PubMed1996

Frequent ectopic expression of a placenta-specific gene at high levels in BALB/c mouse mammary carcinomas.

A placenta-specific gene, MIPP, is transcriptionally regulated in BALB/c mice by a solo long terminal repeat (LTR) of an intracisternal A-particle (IAP), an endogenous retrotransposon. Expression of IAPs, which is also promoted by LTR sequences, is a frequent aberration in many mouse mammary tumors of BALB/c mice. Given that these retroelements and the placental gene have a common promoter, we hypothesized that the tumors also express the gene. Northern blot analysis and RT-PCR revealed high expression of the placenta-specific gene in BALB/c mouse mammary preneoplasias and carcinomas of diverse etiologies, but not in normal mammary gland from virgin, pregnant and lactating mice. The preneoplasias and tumors expressed two transcripts, one of which is apparently unique to the mammary lesions. The other transcript is the same as one expressed in placenta that is not promoted by the IAP LTR. Despite the parallel expression of the placental gene and IAPs in the mammary tissues, RT-PCR showed that LTR sequences are absent from tumor-associated MIPP transcripts. Southern analysis revealed no gross mutations of the MIPP gene in mammary preneoplasias and tumors. The ectopic expression of the placenta-specific gene in BALB/c mouse mammary preneoplasias and carcinomas raises the possibility that it acts as an oncogene.

Animals↗

PubMed1997

LTR retrotransposons and the evolution of eukaryotic enhancers.

Since LTR retrotransposons and retroviruses are especially prone to regional duplications and recombination events, these viral-like systems may be especially conducive to the evolution of closely spaced combinatorial regulatory motifs. Using the Drosophila copia LTR retrotransposon as a model, we show that a regulatory region contained within the element's untranslated leader region (ULR) consists of multiple copies of an 8 bp motif (TTGTGAAA) with similarity to the core sequence of the SV40 enhancer. Naturally occurring variation in the number of these motifs is correlated with the enhancer strength of the ULR. Our results indicate that inter-element selection may favor the evolution of more active enhancers within permissive genetic backgrounds. We propose that LTR retroelements and perhaps other retrotransposons constitute drive mechanisms for the evolution of eukaryotic enhancers which can be subsequently distributed throughout host genomes to play a role in regulatory evolution.

Animals↗

PubMed1997

BARE-ID, a representative of a family of BARE-like elements of the barley genome.

In our search for transposable elements in barley, Hordeum vulgare, we have isolated and cloned two BamHI-fragments of 4.7 and 4.2 kb in length containing very abundant DNA sequences. The 4.7 kb fragment is homologous to the extended region, including more than half of the 5'-LTR and some part of the coding domain of BARE-1, a member of copia-like retrotransposon family of barley. The 4.2 kb fragment, bearing homology to BARE-1 and the WIS-2 family isolated from wheat, is unique among studied retroelements of cereals because it consists of two inverted parts, each containing homology to the LTR and UTL of BARE-1. Functional motifs for reverse transcription, two TATA-boxes and two primer-binding sites, were found within the LTRs. The element contained within this fragment was generated by significant rearrangement of a BARE-like retrotransposon, which included inversion of the extended 5'-terminal region and deletion of the internal domain. Therefore this element is named BARE-ID (BARE-inverted, deleted). A family of BARE-like elements is amplified in the H. vulgare genome compared with wild barley species. The terminal inverted repeat of BARE-ID was used as a probe for examination of evolutionary diversity within genus Hordeum. Our data are basically in agreement with the modern classification system. However, they do not support the combination of H. vulgare and H. bulbosum into one group with the same type of genome. New data concerning the possible origin of the polyploid species, H. secalinum, confirm that retrotransposons are a useful tool for phylogenetic studies.

Base Sequence↗

PubMed2001

Specific pan-neural crest expression of zebrafish Crestin throughout embryonic development.

Zebrafish crestin was identified in a screen for genes dependent on cyclops function and is a member of a family of retroelements (Rubinstein et al. [2000] Genesis 26:86-97). We report here a detailed description of crestin mRNA expression during zebrafish embryogenesis. Crestin expression was first observed during the onset of somitogenesis in cells of the neural crest domain of the ectoderm. Crestin expression was subsequently observed in premigratory cranial and trunk neural crest cells and then in actively migrating crest cells. Cell counts of crestin-expressing premigratory trunk neural crest cells strongly suggest that crestin is expressed by all neural crest cells at this stage. Crestin expression co-localized with a battery of markers for premigratory neural crest cells, developmentally distinct neural crest-derived precursor sublineages, and overtly differentiated neural crest-derived cell types. Expression of crestin is gradually downregulated in overtly differentiated cells. Our results indicate that crestin is a specific pan-neural crest marker throughout zebrafish embryogenesis.

Animals↗

PubMed1997

In vivo production of oligodeoxyribonucleotides of specific sequences: application to antisense DNA.

Retrons, bacterial retroelements found in Gram-negative bacteria, are integrated into the bacterial genome expressing a reverse transcriptase related to eukaryotic reverse transcriptase. The bacterial reverse transcriptases are responsible for the production of multicopy, single-stranded (ms) DNA consisting of a short single-stranded DNA that is attached to an internal guanosine residue of an RNA molecule by a 2',5'-phosphodiester linkage. Reverse transcriptases use an RNA transcript from the retrons, not only as primer, but also as template for msDNA synthesis. By studying the structural requirement, it was found that for msDNA synthesis an internal region of msDNA can be replaced with other sequences. msDNA can thus be used as a vector for in vivo production of an oligodeoxyribonucleotide of a specific sequence. Artificial msDNAs containing a sequence complementary to part of the mRNA for the major outer membrane lipoprotein of Escherichia coli effectively inhibited lipoprotein biosynthesis upon induction of msDNA synthesis. This is the first demonstration of in vivo synthesis of oligodeoxyribonucleotides having antisense function. Since we have previously demonstrated that bacterial retrons are functional in eukaryotes producing msDNA in yeast and in mouse NIH/3T3 fibroblasts, the present system may also be used to produce a specific oligodeoxyribonucleotide inside the cells to regulate eukaryotic gene expression artificially. We also describe a method to produce cDNA to a specific cellular mRNA using the retron system.

Animals↗

PubMed1989

Characterization of the staphylococcal beta-lactamase transposon Tn552.

The staphylococcal beta-lactamase transposon Tn552 is a member of a novel group of transposable elements. The organization of genes in Tn552 resembles that of members of the Tn21 sub-group of Tn3 family transposons, which transpose replicatively by cointegrate formation and resolution. Thus, a possible resolution site ('resL') and a resolvase gene (tnpR or 'binL') have been identified. However, consistent with the fact that Tn552 generates 6 bp (rather than 5 bp) flanking direct repeats of target DNA, neither the putative transposase protein, nor the terminal inverted repeats of Tn552 are homologous to those of Tn3 elements. Tn552, like phage Mu and retroelements, is defined by the terminal dinucleotides 5' TG .. CA 3'. A naturally occurring staphylococcal plasmid, pI9789, contains a Tn552-derived resolution system ('resR-binR') that acts as a 'hotspot' for Tn552 transposition; insertion creates a segment of DNA flanked by inversely repeated resolution sites, one (resR) on pI9789 and the other (resL) on Tn552. The putative Tn552 resolvase, the most closely related of known resolvases to the homologous DNA invertases, initially was identified as a DNA invertase ('Bin') as a result of its ability to mediate efficient inversion of this segment in vivo.

Amino Acid Sequence↗

PubMed1991

Specific expression of the tobacco Tnt1 retrotransposon in protoplasts.

The Tnt1 transposable element of tobacco belongs to the retrotransposon family and shares the structural features of viral retroelements including two long terminal repeats (LTRs) which are known to contain promoter regions. We show that two Tnt1 RNAs of 5.2 and 6.5 kb can be found. The 5.2 kb RNA matches with the size of the Tnt1 elements so far isolated (5.3 kb), whilst the evidence suggests that the 6.5 kb RNA could be a chimaeric RNA initiated in a gene in which Tnt1 has inserted. The Tnt1 5.2 kb RNA starts in the LTR, and the LTR can promote the expression of a translational LTR-beta-glucuronidase (GUS) fusion at a high level in transient expression assays. The Tnt1 5.2 kb RNA and the LTR-GUS fusion of transgenic tobacco plants are specifically expressed in leaf-derived protoplasts whereas they are not expressed in leaf tissue. The 5.2 kb RNA is also transcribed at low levels in roots. This RNA is induced after 2 h of maceration in the protoplast isolation medium, and its level declines rapidly after protoplast isolation. The induction requires only the presence of cell wall hydrolases, and is independent of wounding and plasmolysis. The induction of Tnt1 expression is not mediated by typical oligosaccharide elicitors released from the cell wall known to mediate defense gene responses. Tnt1 transcription features provide a first example of tissue culture-induced mutagenesis in plants and a molecular basis for some of the somaclonal variation events.

Base Sequence↗

PubMed1992

Hepadnaviral assembly is initiated by polymerase binding to the encapsidation signal in the viral RNA genome.

Hepadnaviruses, as well as other pararetroviruses, express their pol (P) gene product unfused to the preceding core gene implying that these retroelements have developed a mechanism for initiating assembly and replication that is principally different from the one used by retroviruses and retrotransposons. We have analysed this mechanism for the human hepatitis B virus by using a newly developed, highly sensitive detection method based upon radiolabelling of the P protein at newly introduced target sites for protein kinase A. The results obtained demonstrate that polymerase encapsidation depends on the concomittant encapsidation of the HBV RNA pregenome and that packaging of the viral RNA, in turn, depends on the presence of P protein. Loss of P protein encapsidation by mutations inactivating the HBV RNA encapsidation signal epsilon could be compensated by trans-complementation with recombinant RNA molecules carrying the epsilon sequence. Thus, in contrast to retroviral replication, the interaction of the hepadnaviral P protein and the RNA genome at its packaging signal appears to be crucial for initiating the formation of replication-competent nucleocapsids. Furthermore, RNA control of P protein packaging stringently limits the number of polymerase molecules that can be encapsidated.

Capsid↗

PubMed1993

Comparative expression of endogenous retrotransposons in adult mouse mammary gland during normal development and differentiation.

Amplified expression of the endogenous retrotransposons, intracisternal A particles (IAPs) and murine leukemia virus-related elements (MLVEs), along with decreased expression of VL30 elements frequently occurs during mouse mammary tumorigenesis. We have now analyzed the expression of these retroelements during the normal developmental and differentiation cycle of the mammary gland as found in virgin, pregnant, lactating, and postlactation adult female BALB/c mice. Retrotransposon expression was either unchanged or decreased during the progressive stages of the cycle compared to virgin tissue. Likewise, growth of mammary epithelial cells in primary culture had little or no effect on expression of IAPs, MLVEs and VL30 sequences. Thus, the dramatic changes involving these retrotransposons in many mouse mammary tumors appear unrelated to any normal state.

Animals↗

PubMed1997

A novel retron that produces RNA-less msDNA in Escherichia coli using reverse transcriptase.

Bacterial retroelements, or retrons, use reverse transcriptase (RT) to produce a multicopy single-stranded DNA (msDNA) molecule that is covalently linked to RNA. In these studies we show that a retron from Escherichia coli 110, a clinical isolate, produces a novel RNA-less msDNA with a 5' phosphate residue. The msDNA is a 74-nucleotide single-stranded DNA molecule with a stable stem-loop structure without a mismatched base pair. Only the genes encoding msDNA (msd), msdRNA (msr), and RT (ret) are required to produce the msDNA molecule. The organization of these genes on the retron was similar to that of other elements producing branched msDNA-RNA. The conserved guanine, which is the branched residue in msDNA-RNA complexes and is essential for branch formation, is also present. Site-directed mutagenesis showed that this guanine is essential for the production of RNA-less msDNA. We postulate that the RNA-less msDNA in strain 110 is produced by nucleolytic cleavage of the branched msDNA-RNA compound.

Amino Acid Sequence↗