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At least 1,567 records · Page 87Linked to original sources
PubMed2000

Three-partner conversion induced by the P-element transposase in Drosophila melanogaster.

Conversion of one P-derived transposon into another has already been shown to occur with a measurable frequency. However, the mechanism responsible for such replacements has remained controversial. We previously proposed a mechanism involving three partners. We assumed that after excision of the P-element inserted at the target site, the double-strand break was repaired using, first, the homologous P sequences on the sister chromatid, and second, a remote template, the donor P-derived transposon. However, two other mechanisms have been proposed. The first involves two partners only, the broken end and the remote template, while the second involves transposition of the donor into the target P-element, followed by a double recombination event. Here we describe the conversion of a defective P-element using as a remote template an enhancer-trap element that is itself unable to transpose because it lacks 21 bp at its 5' end. This result makes it possible to exclude the possibility that this conversion event occurred after transposition. The new allele was molecularly and genetically characterized. The occurrence of a polymorphism at position 33 of the P-element sequence and of an imperfect copy of the template on the 3' side of the converted transposon confirmed that the sister chromatid was absolutely necessary as a partner for repair. Our results show that targeting of a marked P-element is possible, even when this element is unable to transpose. This provides a means of improving recovery of conversion events by eliminating unwanted transpositions catalyzed by the P transposase.

Alleles↗
PubMed2000

P-element transposition in Drosophila melanogaster: influence of size and arrangement in pairs.

In Drosophila melanogaster, several factors have been suggested to influence the rates of P-element transposition and excision, including position effects, size and structure of the elements and differences in transposase source. We have investigated the effect of the size of the starting P-element on the rates of excision and transposition. Four transgenes localized at the same insertion site on the X chromosome and which differ by the number of copies of an internal repeated sequence, were studied. Transgenes with sizes ranging from 11 kb to 22 kb excise at similar rates, and size does not correlate with the differences in transposition rate between them. We also studied the behavior of double P-elements, located at the same site and arranged in various configurations: nested, contiguous or separated by a few base pairs, in the same or reverse orientation. These double P-elements display different mobilities depending on the arrangement of the two transgenes. Transposition and excision rates were also studied for an insertion bearing four transgenes in very close proximity. Our results suggest that several neighboring elements could excise together. We also propose a new model to explain the formation of all the double P-elements we describe.

Animals↗
PubMed2002

Comparison of SXT and R391, two conjugative integrating elements: definition of a genetic backbone for the mobilization of resistance determinants.

The SXT element (SXT) is becoming an increasingly prevalent vector for the dissemination of antibiotic resistances in Vibrio cholerae. SXT is a member of a larger family of elements, formerly defined as IncJ plasmids, that are self-transmissible by conjugation and integrate site-specifically into the host chromosome. Comparison of the DNA sequences of SXT and R391, an IncJ element from Providencia rettgeri, indicate that these elements consist of a conserved backbone that mediates the regulation, excision/integration and conjugative transfer of the elements. Both elements have insertions into this backbone that either confer the element-specific properties or are of unknown function. Interestingly, the conserved SXT and R391 backbone apparently contains hotspots for insertion of additional DNA sequences. This backbone represents a scaffold for the mobilization of genetic material between a wide range of gram-negative bacteria, allowing for rapid adaptation to changing environments.

Base Sequence↗
PubMed2005

Development of a procedure for the sequential extraction of substances binding trace elements in plant biomass.

This work investigates how the amounts of some important substances in a plant, and their behaviour inside the plant, depend on the levels of stress placed on the plant. To this end, model plant spinach (Spinacia oleracea L.) was cultivated on soil treated with sewage sludge. The sewage sludge contained various trace elements (As, Cd, Cu, Zn), and the uptake of these trace elements placed the plant under stress. Following this, a sequential extraction procedure was employed to determine the levels and distributions of trace elements within the most important groups of compounds present in the spinach plants. Since the usual five-step sequential extraction procedure provides only general information on the distributions of elements within individual groups of organic compounds, due to the wide range of organic compounds within the individual fractions, this scheme was extended and improved through the addition of two solvent extraction steps-a butanol step (between the ethyl acetate and methanol solvent steps) and an H(2)O step (after the methanol+H(2)O solvent step). The distributions and levels of the trace elements within the main groups of compounds in spinach biomass was investigated using this new seven step sequential extraction (water free solvents: petroleum ether (A) --> ethyl acetate (B) --> butanol (C) --> methanol (D) --> water solvents: methanol+H(2)O (1+1; v/v) (E) --> H(2)O (F) --> methanol+H(2)O+HCl (49.3+49.3+1.4; v/v/v) (G)). The isolated fractions were characterized using IR spectroscopy and the trace element contents were determined in the individual fractions. Lipophilic compounds with low contents of Cd, Cu and Zn were separated in the first two fractions (A, B). Compounds with higher As contents (11.5-12.8% of total content) were also extracted in the second fraction, B. These two fractions formed the smallest portion of the isolated fractions. Low molecular compounds from secondary metabolism and polar lipids were separated in the third (C) and fourth (D) fractions, and high molecular compounds (mainly polypeptides and proteins) separated in the fifth and sixth fractions (E, F). The addition of the H(2)O solvent step was particularly useful for separating compounds that have a significant impact on trace element bounds. The methanol fraction was dominant for all treatments, and a significant decrease in the spinach biomass separated in this fraction was observed when the soil was treated with sewage sludge. Most of the As (35.5-38.8% of total content), Cu (45.0-51.6%) and Zn (39.8-47.2%) was also determined in this fraction. The G fraction (obtained after acid hydrolysis) contained polar compounds. Most of the Cd was also found in this fraction, as was a significant amount of Zn. Non-extractable residues formed the last fraction (polysaccharides, proteins).

Biomass↗
PubMed2001

A new basal subfamily of mariner elements in Ceratitis rosa and other tephritid flies.

Several copies of highly related transposable elements, Crmar2, Almar1, and Asmar1, are described from the genomes of Ceratitis rosa, Anastrepha ludens, and A. suspensa, respectively. One copy from C. rosa, Crmar2.5, contains a full-length, uninterrupted ORF. All the other copies, from the three species contain a long deletion within the putative ORF. The consensus Crmar2 element has features typical of the mariner/Tc1 superfamily of transposable elements. In particular, the Crmar2 consensus encodes a D,D41D motif, a variant of the D,D34D catalytic domain of mariner elements. Phylogenetic analysis of the relationships of these three elements and other members of the mariner/Tc1 superfamily, based on their encoded amino acid sequences, suggests that they form a new basal subfamily of mariner elements, the rosa subfamily. BLAST analyses identified sequences from other diptera, including Drosophila melanogaster, which appear to be members of the rosa subfamily of mariner elements. Analyses of their molecular evolution suggests that Crmar2 entered the genome of C. rosa in the recent past, a consequence of horizontal transfer.

Amino Acid Sequence↗
PubMed2001

Multi-elemental concentrations in tissues of Japanese common squid (Todarodes pacificus).

Forty-five elements were determined in mantle muscle and liver of juvenile Japanese common squid, Todarodes pacificus, collected from three locations in and near Japanese coasts, using a high-resolution inductively coupled plasma mass spectrometer (HR-ICP-MS) and an inductively coupled plasma atomic emission spectroscope (ICP-AES). Multivariate statistical techniques were applied to discriminate populations of squids from these three locations by treating absolute and relative concentrations of trace elements. Significant differences were found in the concentrations of elements, particularly for some alkaline and alkaline earth elements in the muscle and liver and for some 3d transition elements in the liver of three groups of squids. Squids from the Pacific Ocean could be distinguished from those of the Sea of Japan by discriminant function analysis of elemental concentrations. Based on the analysis, the squids collected from the Nemuro Strait in Japan were predicted to belong to those from the Sea of Japan. Elemental concentrations and discriminant function analysis can be used to identify subpopulations and migratory routes of squids.

Animals↗
PubMed2005

Characterization of a 4 kb variant of the nifD element in Anabaena sp. strain ATCC 33047.

Heterocyst differentiation in some cyanobacteria is accompanied by a programmed DNA rearrangement within the nitrogen fixation gene nifD. The nifD element is excised from within nifD during the latter stages of heterocyst differentiation by site-specific recombination. There is considerable variation in those nifD elements examined thus far, with Nostoc sp. Strain PCC 7120 and Anabaena variabilis having 11 kb elements, and Nostoc punctiforme having a 24 kb element. Here we characterize a 4 kb nifD element in Anabaena sp. Strain ATCC 33047, and compare it with the other sequenced nifD elements. While there is considerable variation in both the size (ranging from 4 kb to 24 kb) and composition of the nifD elements examined thus far, there are regions that are conserved in all. These conserved regions include the flanking 3' and 5' regions, the xisA gene, and a small open reading frame known as ORF2 in Nostoc sp. Strain PCC 7120.

Anabaena↗
PubMed2001

Short interspersed elements (SINEs) from insectivores. Two classes of mammalian SINEs distinguished by A-rich tail structure.

Four tRNA-related SINE families were isolated from the genome of the shrew Sorex araneus (SOR element), mole Mogera robusta (TAL element), and hedgehog Mesechinus dauuricus (ERI-1 and ERI-2 elements). Each of these SINEs families is specific for a single Insectivora family: SOR, for Soricidae (shrews); TAL, for Talpidae (moles and desmans); ERI-1 and ERI-2, for Erinaceidae (hedgehogs). There is a long polypyrimidine region (TC-motif) in TAL, ERI-1, and ERI-2 elements located immediately upstream of an A-rich tail with polyadenylation signals (AATAAA) and an RNA polymerase III terminator (T(4-6)) or TCT(3-4)). Ten out of 14 analyzed mammalian tRNA-related SINE families have an A-rich tail similar to that of TAL, ERI-1, and ERI-2 elements. These elements were assigned to class T+. The other four SINEs including SOR element have no polyadenylation signal and transcription terminator in their A-rich tail and were assigned to class T-. Class T+ SINEs occur only in mammals, and most of them have a long polypyrimidine region. Possible models of retroposition of class T+ and T- SINEs are discussed.

Animals↗
PubMed2003

Zaba: a novel miniature transposable element present in genomes of legume plants.

A novel family of miniature transposable elements, named Zaba, was identified in pea (Pisum sativum) and subsequently also in other legume species using computer analysis of their DNA sequences. Zaba elements are 141-190 bp long, generate 10-bp target site duplications, and their terminal inverted repeats make up most of the sequence. Zaba elements thus resemble class 3 foldback transposons. The elements are only moderately repetitive in pea (tens to hundreds copies per haploid genome), but they are present in up to thousands of copies in the genomes of several Medicago and Vicia species. More detailed analysis of the elements from pea, including isolation of new sequences from a genomic library, revealed that a fraction of these elements are truncated, and that their last transposition probably did not occur recently. A search for Zaba sequences in EST databases showed that at least some elements are transcribed, most probably due to their association with genic regions.

Base Sequence↗
PubMed2003

Genomic characterization of Rim2/Hipa elements reveals a CACTA-like transposon superfamily with unique features in the rice genome.

The availability of huge amounts of rice genome sequence now permits large-scale analysis of the structure and molecular characteristics of the previously identified transposase-encoding Rim2 (also called Hipa) element, which is transcriptionally activated by infection with the fungal pathogen Magnaporthe grisea and by treatment with the corresponding fungal elicitor. Based on genomic cloning and data mining from 230 Mb of rice genome sequence, 347 Rim2 elements, with an average size of 5.8 kb, were identified. This indicates that an estimated total of 600-700 Rim2 elements are present in the whole genome. Rim2 insertions occur non-randomly on the chromosomes, as visualized by fluorescence in situ hybridization. The elements harbor 16-bp terminal inverted repeats with the core sequence CACTG, 16-bp sub-terminal repeats, internal variable regions, 3-bp target sequence duplications in the flanking regions, and genes coding for Rim2 proteins (the putative transposase) and hydroxyproline-rich glycoproteins. High levels of insertion into genic regions are observed for members of this family, and the transposition history of the family can be deduced from the high level of shared sequences and analysis of repeat target sites of the elements. Phylogenetic analysis indicates that the putative RIM2 proteins fall into a subgroup distinct from the TNP2-like subgroup of transposases. Southern hybridization with genomic DNA from monocotyledonous and dicotyledonous plants demonstrates that the RIM2-coding sequence is unique to the Oryza genome. Our results demonstrate that the Rim2 elements from rice belong to a distinct superfamily of CACTA-like elements with evolutionary diversity.

Amino Acid Sequence↗
PubMed2004

The vicinity of a broken chromosome end affects P element mobilization in Drosophila melanogaster.

Broken chromosome ends are believed to be capped by a terminal protein complex, and can be maintained in Drosophila melanogaster for many generations. We investigated whether the vicinity of a chromosome end affected P element mobilization and the subsequent repair of the resulting DNA lesion. High levels of P element excision were observed when at least 5 kb of DNA was located between the P element and the end of the chromosome, but recovery of chromosomes from which the P element had been excised was greatly reduced when the chromosome end was positioned less than 5 kb away from the original P element insertion site. Moreover, when the P element was mobilized in terminal deficiency ( y (TD )) alleles, excision events were accompanied by deletions of sequences originally located distal to the P element.

Animals↗
PubMed1997

Sesqui-Ds, the chromosome-breaking insertion at bz-m1, links double Ds to the original Ds element.

The bz-m1 mutation in maize was one of the first to arise by direct transposition of the chromosome-breaking Ds element from its original or 'standard' location in chromosome 9S to a known locus in the same chromosome arm. Thus, elucidation of its structure should shed light on the nature of the original Ds element described by McClintock in 1948. The Ds insertion in bz-m1 has been reported to be only 1.2 kb long-much shorter than other chromosome-breaking Ds elements that have been described. We have characterized here the Ds element in our bz-m1 stocks and have confirmed by genetic and molecular tests that, in the presence of Ac, it acts as a chromosome breaker. The Ds insertion at bz-m1 is 1260 bp long. Besides its normal 5' and 3' ends, it contains an internal 3' end at the same junction as the chromosome-breaking double Ds element that has been found in several sh mutations. Thus, it appears to have arisen from the 4.1-kb double Ds by internal deletion of 2.9 kb. Because the element has lost one internal 5' end, but retains the chromosome-breaking properties of double Ds, we have named it sesqui-Ds (sDs). The origin, structure and properties of sDs vis-à-vis double Ds support the hypothesis that double Ds corresponds to the chromosome-breaking Ds element at the 'standard' location in 9S.

Amino Acid Sequence↗
PubMed1988

The bacteriophage Mu transposase protein can form high-affinity protein-DNA complexes with the ends of transposable elements of the Tn 3 family.

The 37 kb transposable bacteriophage Mu genome encodes a transposase protein which can recognize and bind to a consensus sequence repeated three times at each extremity of its genome. A subset of this consensus sequence (5'-PuCGAAA(A)-3') is found in the ends of many class II prokaryotic transposable elements. These elements, like phage Mu, cause 5 bp duplications at the site of element insertion, and transpose by a cointegrate mechanism. Using the band retardation assay, we have found that crude protein extracts containing overexpressed Mu transposase can form high-affinity protein-DNA complexes with Mu att R and the ends of the class II elements Tn 3 (right) and IS101. No significant protein-DNA complex formation was observed with DNA fragments containing the right end of the element IS102, or a non-specific pBR322 fragment of similar size. These results suggest that the Mu transposase protein can specifically recognize the ends of other class II transposable elements and that these elements may be evolutionarily related.

Coliphages↗
PubMed1985

The Vi element. A transposon-like repeated DNA sequence interspersed in the vitellogenin locus of Xenopus laevis.

A repeated DNA element in Xenopus laevis is described that is present in about 7500 copies dispersed throughout the genome. It was first identified in the 5' flanking region of one vitellogenin gene and was therefore named the Vi element. Seven copies are present within the vitellogenin gene region, three of them within introns of the genes A1, A2 and B2, and the other four copies in the gene flanking regions. Four of these copies have been sequenced. The Vi element is bounded by a well-conserved 13 base-pair inverted repeat; in addition, it is flanked by a three base-pair direct repeat that appears to be site-specific. The length of these four copies varies from 112 to 469 base-pairs; however, sequence homology between the different copies is very high. Their structural characteristics suggest that length heterogeneity may have arisen by either unequal recombinations, deletions or tandem duplications. Altogether, the characteristics and properties of the Vi element indicate that it might represent a mobile genetic element. One of the four copies sequenced is inserted close (position -535) to the transcription initiation site of the vitellogenin gene B2 in a region otherwise showing considerable homology with the closely related gene B1. Nevertheless, the presence of the Vi element does not seem to influence significantly the estrogen-controlled expression of gene B2. In addition, three alleles of this gene created by length polymorphism in intron 3 and in the Vi element inserted near the transcription initiation site are described.

Animals↗
PubMed1987

Amplification of a chorion gene cluster in Drosophila is subject to multiple cis-regulatory elements and to long-range position effects.

We have used P-element transformation to study cis-acting elements involved in the control of amplification of the third chromosome chorion gene cluster (66D12-15) in Drosophila melanogaster. To reduce position effects large fragments (5.7 to 12 kb; kb = 10(3) bases) of chorion DNA and the 7.2 kb ry+ fragment were used to "buffer" these putative elements from sequences at the insertion site. Nevertheless, even the longest constructs were profoundly affected by the insertion sites and showed amplification levels ranging from undetectable to higher than in the endogenous locus. Any amplification was tissue and temporally correct and extended into the neighboring ry+ sequences. Analysis of amplification levels at various points along two constructs bearing the same 10 kb chorion insert in opposite orientations showed maximal levels occurring at one end of the chorion fragment, irrespective of whether that end was buffered at the middle of the transposon or exposed close to the insertion site. The maximally amplifying region encompasses the amplification control element (ACE), which has been shown to be necessary for amplification, in agreement with its putative role as a replication origin. We have additionally identified amplification-enhancing elements present elsewhere in the 10 kb chorion fragment, which are needed for attainment of high copy number. These elements, distinct from the ACE, have been only coarsely localized within two 2.25 to 2.3 kb regions. Some interesting sequence similarities between these two regions and the ACE element are pointed out.

Animals↗
PubMed1992

Strand-specific LINE-1 transcription in mouse F9 cells originates from the youngest phylogenetic subgroup of LINE-1 elements.

LINE-1 (L1) is a mammalian family of highly repeated DNA sequences that are members of a class of transposable elements whose movement involves an RNA intermediate. Both structural and evolutionary data indicate that the L1 family consists of a small number of active transposable elements interspersed with a large number of L1 pseudogenes. In the mouse, the longest, characterized L1 sequences span about 7000 base-pairs and contain two long open reading frames. Two subfamilies of mouse L1 elements, A and F, have been defined on the basis of the type of putative transcriptional regulatory sequence found at the 5' end. In order to identify a transcribed subset of L1 elements in mouse F9 teratocarcinoma cells, we have examined the strand-specificity of L1 transcription by Northern analysis and compared the open reading frame-1 sequences of ten A-type cDNAs with fifteen genomic A-type L1 elements. Transcripts containing A-type sequence are far more abundant than those containing F-type sequence. Although the majority of L1 RNA in F9 cells appears to be transcribed non-specifically from both strands, our results provide evidence for a subpopulation of variable length, strand-specific transcripts arising from A-type transcriptional regulatory sequences. F9 cell cDNA sequences, which share greater than 99.5% sequence identity with one another, represent a homogeneous subset of the genomic L1 population. Examination of genomic mouse L1 sequences reveals three types of length polymorphism in a defined segment of the first open reading frame. Phylogenetic analysis shows a correlation between the type of length polymorphism in the first open reading frame and the relative age of an individual A-type genomic L1 element. Comparison of the cDNA and genomic sequences indicates that the youngest subgroup of A-type L1 elements is preferentially transcribed in F9 cells. This subgroup may be currently dominating the L1 dispersal process in mice.

Amino Acid Sequence↗
PubMed1990

The U5 sequence is a cis-acting repressive element for genomic RNA expression of human T cell leukemia virus type I.

The long terminal repeat (LTR) of HTLV-1 consists of U3-R-U5 and contains elements which regulate the viral gene expression. In addition to these elements, we found that the U5 sequence contained a repressive element in the gene expression. Sequential deletions of the LTR substantially increased CAT expression of a LTR-CAT construct. The repressive effect was also observed at RNA level on unspliced RNA, but not on spliced RNA. These differential effects suggest that the U5 element is a cis-acting RNA element, since splicing within the R segment removed the U5 element. In the context of HTLV-1 gene expression, the U5 element would repress expression of unspliced genomic RNA of HTLV-1, but not subgenomic RNA.

Cell Line↗
PubMed1995

Review of trace elements in blood, serum and urine for the Czech and Slovak populations and critical evaluation of their possible use as reference values.

The availability of accurate trace element reference values in human tissues represents an important indicator to the health status of the general population and occupational groups exposed to trace elements. The EURO TERVIHT project (Trace Element Reference Values in Human Tissues) aims to establish and compare trace element reference values in tissues from inhabitants of the European countries as baseline values for clinical/toxicological assessment studies. In this context, one of the first steps considered is the critical evaluation (state of the art) of existing literature on trace element reference values in blood, serum and urine in the general population of each European country. This paper reviews the Czech and Slovak situation by assessing studies carried out in these countries for Al, As, Cd, Co, Cr, Cu, F, Mn, Hg, Ni, Pb, Rb, Sc, Se, V and Zn in blood, serum and urine. These studies show that most of the data available do not meet criteria designed recently for deriving reference intervals, especially regarding the number of subjects, the age of population sample studies as well as the use of appropriate sampling techniques and quality assurance procedures. Elements which present the highest potential risk for health in Czech and Slovak populations and for which reference values should be urgently established are: Cd, Hg, Pb (major pollutants); As, Cr, Ni (carcinogenic metals); Al, F, Mn, Tl, V (released into the environment by coal combustion and other industrial activities); Pt (increasing use of Pt catalyst in petrol-driven automobiles); essential trace elements such as I, Se and Zn for which a deficiency in Czech and Slovak populations was detected or is suspected.

Czechoslovakia↗