Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “mobile elements”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 721 records · Page 40Linked to original sources
PubMed2006

Cloning of the organophosphorus pesticide hydrolase gene clusters of seven degradative bacteria isolated from a methyl parathion contaminated site and evidence of their horizontal gene transfer.

Seven organophosphorus pesticide-degrading bacteria harboring the methyl parathion degrading (mpd) gene were isolated from a methyl parathion contaminated site. In this study, the 4.7 kb mpd gene cluster, conserved in all seven bacteria capable of degrading methyl parathion, was cloned and further analysis revealed that this cluster contained five ORFs and the mpd gene was associated with a mobile element, IS6100. In addition to mpd gene ORF and tnpA ORF, three other ORFs showed high homology to the permease component of ABC-type transport system, the general secretion pathway protein B, and the RNA polymerase sigma 70 factor, respectively. The mpd genes of these 7 strains were subcloned and expressed in E. coli, SDS-PAGE and zymogram analysis showed that two expression products of mpd genes in E. coli were found, but the one without signal peptide showed the hydrolytic activities. Our evidences collectively suggest that mpd gene cluster may be disseminated through horizontal gene transfer based on phylogenetic analysis of the cluster and their host bacterial strains, and comparisons of GC content of the cluster and respective host's chromosome.

Aryldialkylphosphatase↗
PubMed2004

Diversity of structure and function of DNA polymerase (gp43) of T4-related bacteriophages.

The replication DNA polymerase (gp43) of the bacteriophage T4 is a member of the pol B family of DNA polymerases, which are found in all divisions of life in the biosphere. The enzyme is a modularly organized protein that has several activities in one polypeptide chain (approximately 900 amino acid residues). These include two catalytic functions, POL (polymerase) and EXO (3 -exonuclease), and specific binding activities to DNA, the mRNA for gp43, deoxyribonucleotides (dNTPs), and other T4 replication proteins. The gene for this multifunctional enzyme (gene 43) has been preserved in evolution of the diverse group of T4-like phages in nature, but has diverged in sequence, organization, and specificity of the binding functions of the gene product. We describe here examples of T4-like phages where DNA rearrangements have created split forms of gene 43 consisting of two cistrons instead of one. These gene 43 variants specify separate gp43A (N-terminal) and gp43B (C-terminal) subunits of a split form of gp43. Compared to the monocistronic form, the interruption in contiguity of the gene 43 reading frame maps in a highly diverged sequence separating the code for essential components of two major modules of this pol B enzyme, the FINGERS and PALM domains, which contain the dNTP binding pocket and POL catalytic residues of the enzyme. We discuss the biological implications of these gp43 splits and compare them to other types of pol B splits in nature. Our studies suggest that DNA mobile elements may allow genetic information for pol B modules to be exchanged between organisms.

Animals↗
PubMed2005

Molecular mechanisms of epigenetics.

The main epigenetic mechanisms in regulation of gene expression are discussed. The definition of epigenetics and its specific mechanisms including DNA methylation and gene imprinting, modifications of nucleosomal histones associated with silencing or activation of gene transcription, RNA interference, chromosomal silencing, and the role of mobile elements are discussed.

Acetylation↗
PubMed2005

Molecular and chromosomal analysis of ribosomal cistrons in two cartilaginous fish, Taeniura lymma and Raja montagui (Chondrichthyes, Batoidea).

We used silver nitrate staining, CMA3 and FISH to study the chromosomal localization of both the major ribosomal genes and the nucleolar organizer regions as well as that of the minor ribosomal genes (5S rDNA) in two species of Batoidea, Taeniura lymma (Dasyatidae) and Raja montagui (Rajidae). In both species, all the metaphases examined showed the presence of multiple NOR-bearing sites, while the gene for 5S rRNA proved to be localized on two chromosome pairs. Furthermore, one of the two 5S rDNA sites in T. lymma was shown to be co-localized with the major ribosomal cluster. The presence of multiple nucleolar organizer regions in the two species might be interpreted as being the result of intraspecific polymorphisms, or as a phenomenon of the amplified transposition of mobile elements of the genome. We also determined the nucleotide sequence of the 5S rRNA gene, consisting of 564 bp in R. montagui and 612 bp in T. lymma. We also found TATA-like and (TGC)n trinucleotides, (CA)n dinucleotides and (GTGA)n tetranucleotides, which probably influence gene regulation.

Animals↗
PubMedDate not supplied

Interplasmid transposition demonstrates piggyBac mobility in vertebrate species.

The piggyBac transposon is an extremely versatile helper-dependent vector for gene transfer and germ line transformation in a wide range of invertebrate species. Analyses of genome sequencing databases have identified piggyBac homologues among several sequenced animal genomes, including the human genome. In this report we demonstrate that this insect transposon is capable of transposition in primate cells and embryos of the zebrafish, Danio rerio. piggyBac mobility was demonstrated using an interplasmid transposition assay that has consistently predicted the germ line transformation capabilities of this mobile element in several other species. Both transfected COS-7 primate cells and injected zebrafish embryos supported the helper-dependent movement of tagged piggyBac element between plasmids in the characteristic cut-and-paste, TTAA target-site specific manner. These results validate piggyBac as a valuable tool for genetic analysis of vertebrates.

Animals↗
PubMed1987

Adjacent satellite DNA segments in Drosophila structure of junctions.

The structure of eight satellite DNA molecules containing a junction between tandem arrays of different repeated sequences is described. In one class of junctions there was an abrupt switch with the juxtaposition of two satellite arrays. These arrays were closely related and the periodicity of repeats was maintained in phase across the junction. These arrays usually showed extreme homogeneity in their repeating sequences. A second class of junctions was more complex, and in two cases may have arisen by the insertion of a mobile element into a satellite array. A novel mechanism of satellite formation is proposed to explain the precision of junctions and sequence similarities of neighboring satellite arrays. Homogeneous satellite arrays would be generated enzymatically by synthesis of a repeat using the preceding repeat as template. Occasional errors in copying of the template, either single base changes or misreading the length of the repeat unit, would lead to abrupt switches in the repeating sequence.

Animals↗
PubMed1989

Isolation and characterization of ribosomal DNA variants from Sciara coprophila.

The ribosomal RNA multigene family in the fungus fly Sciara coprophila contains a total of only 65 to 70 repeat units. We explored the types and frequencies of variant repeats in this small multigene family by characterizing different cloned rDNA variants from Sciara. Although we did not observe any intergenic spacer length variants in Sciara, we found a variant due to the insertion of a putative mobile element (lambda Bc11), and variants containing ribosomal insertion elements. By DNA sequence analysis of rDNA/non-rDNA junctions, there are three distinct types of ribosomal insertion elements found in Sciara rDNA: two correspond to the R1 and R2 insertion elements found in other dipterans (clones lambda Bc5 and pBc1L1, respectively), and one is a novel class of ribosomal insertion elements (R3, exemplified by clone pBc6D6) which so far is unique to Sciara. Together, the several different rDNA variants make up from 12 to 20% of the rDNA in Sciara. These results are discussed in the context of evolution of the ribosomal RNA multigene family.

Animals↗
PubMed1991

Six group I introns and three internal transcribed spacers in the chloroplast large subunit ribosomal RNA gene of the green alga Chlamydomonas eugametos.

The chloroplast large subunit rRNA gene of Chlamydomonas eugametos and its 5' flanking region encoding tRNA(Ile) (GAU) and tRNA(Ala) (UGC) have been sequenced. The DNA sequence data along with the results of a detailed RNA analysis disclosed two unusual features of this green algal large subunit rRNA gene: (1) the presence of six group I introns (CeLSU.1-CeLSU.6) whose insertion positions have not been described previously, and (2) the presence of three short internal transcribed spacers that are post-transcriptionally excised to yield four rRNA species of 280, 52, 810 and 1720 nucleotides, positioned in this order (5' to 3') in the primary transcript. Together, these RNA species can assume a secondary structure that is almost identical to that proposed for the 23 S rRNA of Escherichia coli. All three internal transcribed spacers map to variable regions of primary sequence and/or potential secondary structure, whereas all six introns lie within highly conserved regions. The first three introns are inserted within the sequence encoding the 810 nucleotide rRNA species and map within domain II of the large subunit rRNA structure; the remaining introns, found in the sequence encoding the 1720 nucleotide rRNA species, lie within either domain IV or V, as is the case for all other large subunit rDNA introns that have been documented to date. CeLSU.5 and CeLSU.6 each contain a long open reading frame (ORF) of more than 200 codons. While the CeLSU.6 ORF is not related to any known ORFs, the CeLSU.5 ORF belongs to a family of ORFs that have been identified in Podospora and Neurospora mitochondrial group I introns. The finding that a polymorphic marker showing unidirectional gene conversion during crosses between C. eugametos and Chlamydomonas moewusii is located within the CeLSU.5 ORF makes it likely that this intron is a mobile element and that its ORF encodes a site-specific endonuclease promoting the transfer of the intron DNA sequence.

Amino Acid Sequence↗
PubMed1983

Telomere regions in Drosophila share complex DNA sequences with pericentric heterochromatin.

A 12 kb fragment of Drosophila melanogaster DNA cloned in a lambda phage, lambda T-A, is shown by in situ hybridization to contain sequences homologous to DNA at the extreme ends of each of the polytene chromosomes and to the pericentric sequences present in the beta heterochromatin. This pattern of hybridization is seen for each of the four D. melanogaster stocks that have been studied. Most of the sequence in lambda T-A shows no detectable homology to DNA within the banded chromosome arms. (The only exception is what appears to be a short mobile element inserted in lambda T-A. This portion of lambda T-A hybridizes with internal arm sites that vary from stock to stock). Analysis of restriction fragments of genomic DNA indicates that the sequences in lambda T-A are homologous to complex sets of repeated sequences that differ from stock to stock in D. melanogaster. Some, but not all, of the members of these sets are underreplicated during polytenization in D. melanogaster. The sequences in lambda T-A are also homologous to complex sets of repeated sequences in the genomes of other Drosophila species belonging to the melanogaster species group. Pericentric and telomeric localization is conserved in these related species, although analysis of DNA fragments shows marked changes in sequence organization on a finer scale. The constancy of the localization of lambda T-A-homologous sequences to telomeric and pericentric regions suggests that these sequences serve a function in those regions.

Animals↗
PubMed1985

An insertion within a variably spliced Drosophila tropomyosin gene blocks accumulation of only one encoded isoform.

We have characterized an aberrant allele of a variably spliced Drosophila tropomyosin gene. The allele was recovered from the flightless Ifm(3)3 strain, which has been shown to have structurally and functionally abnormal indirect flight muscles. The transcribed portion of the mutant gene is interrupted by an 8,8 kb insertion of middle repetitive DNA having a structure typical of copia-like Drosophila mobile elements. The insertion is positioned so as to interrupt an exon sequence in one splicing mode and, simultaneously, an intron in the alternate mode. As a consequence of the insertion the allele fails to direct synthesis of the flight muscle-specific tropomyosin isoform, but remains capable of specifying a second isoform, which accumulates in nonfibrillar Drosophila muscles.

Alleles↗
PubMed1989

A mobile group I intron in the nuclear rDNA of Physarum polycephalum.

We have shown that a strain-specific group I intron (intron 3) in the nuclear extrachromosomal rDNA or Physarum polycephalum is a mobile element. Shortly after mating of amoebae from intron-lacking and intron-containing strains, intron 3 transposes in a site-specific manner into all available recipient molecules. The transposition appears to occur by gene conversion, as evidence by the co-conversion of adjacent sequences and by double strand breakage observed in some of the recipient rDNA molecules. We infer that the double strand break is induced by an endonuclease encoded by intron 3, since in vitro transcription and translation of the cloned intron leads to the synthesis of an enzymatically active, site-specific nuclease. This is the first demonstration of the transposition of a nuclear intron in an experimental setting, and provides a rare example of a protein encoded by an RNA polymerase I transcript.

Base Sequence↗
PubMedDate not supplied

Mutagenic effects of some water-soluble metal compounds in a somatic eye-color test system in Drosophila melanogaster.

Nickel, cadmium, lead, arsenic, manganese and chromium salts as well as MeHgOH were screened for mutagenicity, using a sensitive somatic eye-color test system in Drosophila melanogaster. The test is based on the insertion of a mobile element which causes instability in the white locus that is somatically enhanced by mutagens. This white locus expression is combined with a mutation, zeste, in another gene, to produce a light yellow eye color. Larval feeding with mutagens causes somatic mutations in the eye imaginal disc cells that develop into easily detectable red spots in the yellow eyes of adult males. Survival tests showed large differences in the toxicity of different metals, but only hexavalent chromium increased the frequency of somatic mutations above the control level. When combined treatments were carried out with MMS and various metals, sodium arsenite caused a reduction of the MMS-induced mutation frequency while methylmercury increased the frequency of somatic spots.

Animals↗
PubMed1982

The pUC plasmids, an M13mp7-derived system for insertion mutagenesis and sequencing with synthetic universal primers.

A series of plasmid vectors containing the multiple cloning site (MCS7) of M13mp7 has been constructed. In one of these vectors a kanamycin-resistance marker has been inserted into the center of the symmetrical MCS7 to yield a restriction-site-mobilizing element (RSM). The drug-resistance marker can be cleaved out of this vector with any of the restriction enzymes that recognize a site of the flanking sequences of the RSM to generate an RSM with either various sticky ends or blunt ends. These fragments can be used for insertion mutagenesis of any target molecule with compatible restriction sites. Insertion mutants are selected by their resistance to kanamycin. When the drug-resistance marker is removed with PstI, a small in-frame insertion can be generated. In addition, two new MCSs having single restriction sites have been formed by altering the symmetrical structure of MCS7. The resulting plasmids pUC8 and pUC9 allow one to clone doubly digested restriction fragments separately with both orientations in respect to the lac promoter. The terminal sequences of any DNA cloned in these plasmids can be characterized using the universal M13 primers.

Base Sequence↗
PubMed1985

Structural organization of rat ribosomal RNA genes: interspersed sequences and their putative role in the alignment of nucleosomes.

We have observed four regions containing highly repetitive interspersed sequences in the nontranscribed spacer (NTS) of the rat rRNA genes. Two of them (A and B) are located at a distance of 3-5 kb upstream from the transcription start point and two others (C and D) at a distance of 2-5 kb downstream from the 3' end of the 28S rRNA gene. These repetitive sequences are widely dispersed in the genome and are included both in small-copy regions and in the families of extended reiterated sequences. The sequences of three fragments were determined: one from the C2 region, 1100 bp in length and two from A and C1 regions, 110-120 bp long. These regions are characterized by the presence of 'simple' sequences, such as (AC)n, (ACC)n, (GAG)n, (GGGA)n, (TAAG)n, and also of long blocks, (G)n and (A)n. In the C2 region two palindromes, 16 and 14 nt long, were found, one of them including a XhoI site. Mobile element B2 was observed in regions B and C. All four regions, A, B, C and D, contain sets of simple sequences, among which some common elements have been found. Theoretical prediction of the nucleosomal disposition in the C region indicates that the combination of simple sequences existing in the given area secures fixed positions of the nucleosomes, one of the nucleosomes being formed on the B2 element. Moreover, a striking periodicity, with the repeat length close to that of the rat nucleosomal DNA, has been observed. A hypothesis is put forward that the simple sequences can dictate the location of nucleosomes on the adjoining DNA sequences, thereby regulating the gene activity.

Animals↗
PubMed1985

Insertion of a long KpnI family member within a mitochondrial-DNA-like sequence present in the human nuclear genome.

Structural analysis of a phage lambda Charon 4A clone carrying one of the human nuclear mitochondrial(mut)-DNA-like sequences revealed that a KpnI-family member (KpnI 5.5-kb DNA) is inserted within this sequence. The inserted KpnI 5.5-kb DNA contains several possible polyadenylation signal sequences followed by an A-rich sequence at its 3' end and is flanked by perfect 13-bp direct repeats of the duplicated mtDNA-like sequences. These structures strongly suggest that the KpnI 5.5-kb DNA is a mobile element. Comparison of the 5' terminal sequences of the KpnI 5.5-kb DNA and four other long KpnI-family DNAs so far examined, using the predicted general promoter sequence for eukaryotic tRNAs, indicates that they contain the consensus sequences for the split internal RNA polymerase III control region.

Base Sequence↗
PubMed1993

Engineering of alkyl- and haloaromatic-responsive gene expression with mini-transposons containing regulated promoters of biodegradative pathways of Pseudomonas.

Four recombinant mini-Tn5 transposons are described which contain outward-facing Pm, Pu or Psal promoters from the catabolic plasmids TOL and NAH of Pseudomonas putida, along with their cognate wild-type regulatory genes (xylS, xylR, nahR) or mutant varieties (xylS2). Transcription from such promoters is activated when the host bacteria encounters certain aromatic compounds, such as alkyl- and halobenzoates (XylS, XylS2), alkyl- and halotoluenes (XylR) or salicylates (NahR). These transposons enable the generation of conditional phenotypes dependent on the presence of specific effectors, as well as the engineering of strains expressing heterologous genes that are regulated by aromatic inducers. A mini-Tn5 xylS/Pm::luxAB, was used to construct Pseudomonas strains emitting light upon exposure to concentrations of m-toluate as low as 5-10 microM. The broad-host-range transposition system of Tn5 and the stability of the inserted genes due to the loss of the transposase-encoding gene during delivery of the mobile element make these transposons particularly well suited for the construction of stable strains exhibiting halo/alkyl aromatic-regulated conditional phenotypes in the absence of antibiotic selection, as is required for some uncontained bioremediation and biomonitoring applications.

Benzoates↗
PubMed1995

Bovine Alu-like sequences mediate transposition of a new site-specific retroelement.

We describe a new family of 3.1-kb repetitive sequences which is present in the bovine genome. The 5' and 3' ends of the unit are flanked with sequences homologous to the 5' and 3' halves of the bovine Alu-like monomer (BM), respectively. Distribution of the 5' ends of the family members in the genome is not random. They are close to the truncated bovine Alu-like dimer (BD) which, in some cases, is followed by 40-bp repeated sequences containing block A of the RNA polymerase III promoter. The ORFs found within the unit code for peptides homologous to amino-acid sequences characteristic for reverse transcriptases (RT). The family members may be considered as mutant mobile elements whose propagation in the genomes was accomplished by means of a process including site-specific recognition with BD. Because of this, we call this family the bovine dimer-driven family (BDDF).

Amino Acid Sequence↗
PubMed1995

A transposon-like sequence adjacent to the AccI restriction-modification operon.

We have cloned and sequenced the accIRM genes from Weeksella zoohelcum (the original identification of this strain as Acinetobacter calcoaceticus was incorrect). Our sequence differs in the coding regions from a previously published sequence by the addition of three nucleotides near the 3' end of the DNA methyltransferase-encoding gene (accIM). We have sequenced approx. 3 kb beyond this operon. Two genes were found, convergently transcribed with the R-M operon. The first of these genes encodes a protein which shows significant similarity to the recombinases of the phage integrase family. The W. zoohelcum recombinase may function as a transposon resolvase, as in Tn4430. The recombinase-encoding gene is followed by a putative transposase (Tnp), which is in turn followed by a terminator which is predicted to be Rho-dependent for the recombinase-Tnp operon and Rho-independent for the convergent R-M operon. Since the G + C content of the two operons is notably different, it is possible that the terminator is at the extremity of the mobile element and serves to protect it from incoming transcription.

Amino Acid Sequence↗