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 631 records · Page 35Linked to original sources
PubMed2004

Structure and dynamics of Candida rugosa lipase: the role of organic solvent.

The effect of organic solvent on the structure and dynamics of proteins was investigated by multiple molecular dynamics simulations (1 ns each) of Candida rugosa lipase in water and in carbon tetrachloride. The choice of solvent had only a minor structural effect. For both solvents the open and the closed conformation of the lipase were near to their experimental X-ray structures (C(alpha) rms deviation 1-1.3 A). However, the solvents had a highly specific effect on the flexibility of solvent-exposed side chains: polar side chains were more flexible in water, but less flexible in organic solvent. In contrast, hydrophobic residues were more flexible in organic solvent, but less flexible in water. As a major effect solvent changed the dynamics of the lid, a mobile element involved in activation of the lipase, which fluctuated as a rigid body about its average position. While in water the deviations were about 1.6 A, organic solvent reduced flexibility to 0.9 A. This increase rigidity was caused by two salt bridges (Lys85-Asp284, Lys75-Asp79) and a stable hydrogen bond (Lys75-Asn 292) in organic solvent. Thus, organic solvents stabilize the lid but render the side chains in the hydrophobic substrate-binding site more mobile. [figure: see text]. Superimposition of open (black, PDB entry 1CRL) and closed (gray, PDB entry 1TRH) conformers of C. rugosa lipase. The mobile lid is indicated.

Candida↗
PubMed2000

Reduced neurological injury during CABG in patients with mobile aortic atheromas: a five-year follow-up study.

BACKGROUND: Mobile atheromas of the thoracic aorta have been identified as a major cause of stroke after coronary artery bypass grafting (CABG). This prospective study was undertaken to identify mobile atheromas and to determine the incidence of immediate postoperative embolic events after suitable surgical modifications. Late clinical events attributable to embolization were also studied. METHODS: Between January 1993 and July 1997, 3,660 patients scheduled for CABG underwent intraoperative transesophageal echocardiography to identify aortic atheromatous disease. The disease was graded as follows: grade I, plaques extending less than 5 mm into the aortic lumen; grade II, plaques extending more than 5 mm into the aortic lumen; and grade III, plaques with a mobile element. Only patients with grade III atheromas were included in the study. Various surgical modifications were done depending on the location of the lesion, eg, aortic arch atherectomy, CABG combined with transmyocardial laser revascularization, off-pump CABG by median sternotomy, and minimally invasive direct coronary artery bypass. Measured outcomes were death, stroke, and other vascular events, both early (within 1 week) and late (1 to 5 years) after operation. RESULTS: Of the 3,660 patients, 104 (2.84%) had mobile atheromas. The perioperative stroke rate was 0.96%, and the incidence of other vascular events was 1.92% at 1 week. There was no embolic event in the group of 88 patients who underwent off-pump CABG. Of the study group, 98.07% are in regular follow-up. At 5 years, 1 patient had had a nonfatal stroke, and 2 patients had died of causes unrelated to atheromatous disease. CONCLUSIONS: The stroke rate was very low in patients with mobile aortic atheromas who underwent CABG after modification in surgical technique, especially off-pump CABG. A follow-up of 5 years showed that patients with mobile atheromas have a very low incidence of spontaneous embolization.

Adult↗
PubMed2006

PLOTREP: a web tool for defragmentation and visual analysis of dispersed genomic repeats.

Identification of dispersed or interspersed repeats, most of which are derived from transposons, retrotransposons or retrovirus-like elements, is an important step in genome annotation. Software tools that compare genomic sequences with precompiled repeat reference libraries using sensitive similarity-based methods provide reliable means of finding the positions of fragments homologous to known repeats. However, their output is often incomplete and fragmented owing to the mutations (nucleotide substitutions, deletions or insertions) that can result in considerable divergence from the reference sequence. Merging these fragments to identify the whole region that represents an ancient copy of a mobile element is challenging, particularly if the element is large and suffered multiple deletions or insertions. Here we report PLOTREP, a tool designed to post-process results obtained by sequence similarity search and merge fragments belonging to the same copy of a repeat. The software allows rapid visual inspection of the results using a dot-plot like graphical output. The web implementation of PLOTREP is available at http://bioinformatics.abc.hu/PLOTREP/.

Computer Graphics↗
PubMed2000

The 51,409-bp R-plasmid pTP10 from the multiresistant clinical isolate Corynebacterium striatum M82B is composed of DNA segments initially identified in soil bacteria and in plant, animal, and human pathogens.

The 51,409-bp DNA sequence of the multiresistance plasmid pTP10 from the gram-positive opportunistic human pathogen Corynebacterium striatum M82B has been determined. Fully automated genome interpretation led to the identification of 47 ORFs. Analysis of the genetic organization of pTP10 suggests that the plasmid is composed of eight DNA segments, the boundaries of which are represented by transposons and insertion sequences. The DNA segments of pTP10 are highly similar to (1) a plasmid-encoded erythromycin resistance region from the human pathogen Corynebacterium diphtheriae; (2) a chromosomal DNA region from Mycobacterium tuberculosis; (3) a plasmid-encoded chloramphenicol resistance region from the soil bacterium Corynebacterium glutamicum; (4) transposable elements from phytopathogenic gram-negative Pseudomonas, Xanthomonas and Erwinia species; and (5) a plasmid-encoded aminoglycoside resistance region from the gram-negative fish pathogen Pasteurella piscicida. The complete DNA sequence of pTP10 provides genetic information regarding the mechanisms of resistance to 16 antimicrobial agents that belong to six structural classes. In addition, the mosaic structure of pTP10 represents the evolutionary consolidation into a single plasmid molecule of antimicrobial resistances from microorganisms found in different habitats by means of mobile elements, resulting in the generation of a multiresistant bacterium that can infect humans.

Animals↗
PubMed1997

Burdock, a novel retrotransposon in Drosophila melanogaster, integrates into the coding region of the cut locus.

The burdock element is known to be the 2.6-kb insertion into the same region of the cut locus in 12 independently obtained ct-lethal mutants. Here we have determined the complete sequences of this insertion and of the hot spot region. It was found that the burdock is a short retrotransposon with long terminal repeats and a single open reading frame (ORF). The polypeptide encoded by the burdock ORF contains two adjacent regions homologous to the gag and pol polyproteins of the gypsy mobile element. The burdock insertion interrupts the short ORF of the cut locus. The target site sequence of the burdock insertions is similar to the Drosophila topoisomerase II cleavage site.

Amino Acid Sequence↗
PubMed2006

ISPa20 advances the individual evolution of Pseudomonas aeruginosa clone C subclone C13 strains isolated from cystic fibrosis patients by insertional mutagenesis and genomic rearrangements.

Pseudomonas aeruginosa clone C strains, which chronically colonize the lungs of cystic fibrosis patients reorganize their genome structure. In this study, a novel member of the IS3 subfamily of IS elements, ISPa20, was detected which was specific for clone C subclone C13 strains. ISPa20, which was present in high copy number, mediated events of genomic reorganization. ISPa20 was inserted into P. aeruginosa backbone genes leading to adaptation to the cystic fibrosis lung habitat and into DNA acquired through horizontal gene transfer. Further on, large chromosomal inversions were mediated by ISPa20. In contrast to strains of other subclonal linages high rates of genomic rearrangements of subclone C13 strains were observed in vitro. The acquisition of mobile elements by P. aeruginosa clone C strains in the lungs of cystic fibrosis patients supports the chronic colonization by insertional mutagenesis and chromosome restructuring leading to microevolution within clone C that reflects macroevolution observed on the species level.

Chromosome Inversion↗
PubMed2001

Certification of the extractable contents of Cd, Cr, Cu, Ni, Pb and Zn in a freshwater sediment following a collaboratively tested and optimised three-step sequential extraction procedure.

Sequential extraction procedures have been used during the last decades to study and determine trace element mobility in aquatic sediments. However, the results obtained are operationally defined and, therefore, the significance of the analytical results is related to the extraction scheme used. So, there is a need for suitable reference materials for this type of study to enable the validation of the methodologies and to control the quality of the measurements. This paper describes the preparation of a sediment reference material, BCR-701, the homogeneity and stability studies and the analytical work performed for the certification of the extractable contents of some trace elements, following a collaboratively tested and optimised sequential (three-step) extraction procedure. The paper contains all the results and gives the methods used to certify the extractable contents (mass fractions expressed as mg kg-1 on a dry matter basis) of Cd, Cr, Cu, Ni, Pb and Zn in all steps. Moreover, indicative values are given for the aqua regia extractable contents of the six elements in the sediment and the residue obtained after sequential extraction.

Chemistry Techniques, Analytical↗
PubMed2005

Bap: a family of surface proteins involved in biofilm formation.

A group of surface proteins sharing several structural and functional features is emerging as an important element in the biofilm formation process of diverse bacterial species. The first member of this group of proteins was identified in a Staphylococcus aureus mastitis isolate and was named Bap (biofilm-associated protein). As common structural features, Bap-related proteins: (i) are present on the bacterial surface; (ii) show a high molecular weight; (iii) contain a core domain of tandem repeats; (iv) confer upon bacteria the capacity to form a biofilm; (v) play a relevant role in bacterial infectious processes; and (vi) can occasionally be contained in mobile elements. This review summarizes recent studies that have identified and assigned roles to Bap-related proteins in biofilm biology and virulence.

Bacteria↗
PubMed1996

Native DNA repeats and methylation in Ascobolus.

We identified two classes of native dispersed DNA repeats in the Ascobolus genome. The first class consisted of several kilobase long, methylated repeats. These repeats, named Mars (methylated Ascobolus repeated sequences), fell in one family of LINE-like elements and in three families of LTR-containing retrotransposable elements. The methylation features of Mars elements were those expected if they were natural targets for the MIP (methylation induced premeiotically) previously discovered in Ascobolus. The second class consisted of short repeats, approximately 100 bp long, corresponding to 5S rRNA and tRNA genes. As expected from their size, which was too small to allow MIP to occur, they were unmethylated, as were 26 kb of unique sequences tested. These observations are consistent with the hypothesis that MIP is targeted at natural DNA repeats and constitutes a defensive process against the detrimental consequences of the spreading of mobile elements throughout the genome. The 9 kb tandem repeats harbouring the 28S, 18S and 5.8S rRNA genes displayed methylation features suggesting that rDNA methylation proceeds through a process other than MIP.

Amino Acid Sequence↗
PubMed2004

Regulated site-specific recombination of the she pathogenicity island of Shigella flexneri.

The she pathogenicity island (PAI) is a chromosomal, laterally acquired, integrative element of Shigella flexneri that carries genes with established or putative roles in virulence. We demonstrate that spontaneous, precise excision of the element from its integration site in the 3' terminus of the pheV tRNA gene is mediated by an integrase gene (int) and a gene designated rox (regulator of excision), both of which are carried on the she PAI. Integrase-mediated excision occurs via recombination between a 22 bp sequence at the 3' terminus of pheV and an imperfect direct repeat at the pheV-distal boundary of the PAI. Excision leads to the formation of a circular episomal form of the PAI, reminiscent of circular excision intermediates of other mobile elements that are substrates for lateral transfer processes such as conjugation, packaging into phage particles and recombinase-mediated integration into the chromosome. The circle junction consists of the pheV-proximal and pheV-distal boundaries of the PAI converging on a sequence identical to 22 bp at the 3' terminus of pheV. The isolated circle was transferred to Escherichia coli where it integrated specifically into phe tRNA genes, as it does in S. flexneri, independently of recA. We also demonstrate that Rox stimulates, but is not essential for, excision of the she PAI in an integrase-dependent manner. However, Rox does not stimulate excision by activating the transcription of the she PAI integrase gene, suggesting that it has an excisionase function similar to that of a related protein from the P4 satellite element of phage P2.

Animals↗
PubMed1991

Properties of the spectrin-like structural element of smooth-muscle alpha-actinin.

The fragment of smooth muscle alpha-actinin, comprising the four spectrin-like structural repeating units, has a high alpha-helix content, similar to that of spectrin, and a hydrodynamic frictional coefficient, indicative of an elongated, probably bent or kinked rod-like structure, as found for spectrin dimer and tetramer. The fragment exists in solution as an extremely stable dimer, which is dissociated only under denaturing conditions and is much more resistant to dissociation by urea than is the spectrin heterodimer. High-resolution proton magnetic resonance spectra reveal that a part of the polypeptide chain gives rise to sharp resonances; this is also true of spectrin and it implies that the individual structural repeating units contain segmentally mobile elements, which may be required to generate the elastic properties of the spectrin family of proteins. Again like spectrin, the alpha-actinin fragment contains multiple binding sites for long-chain fatty acids, as revealed by quenching of tryptophan fluorescence by 2-bromostearate (though not by 9(10)-bromostearate). The results point to extensive structural and functional similarities between the repeating units of all the proteins of the spectrin family.

Actinin↗
PubMedDate not supplied

A transposon-like element in human DNA.

Mobile genetic elements have been reported in prokaryotes, plants, yeast and Drosophila. The only transposon-like sequences reported for mammalian organisms are closely related to retroviruses, although undoubtedly other transposon families exist within the mammalian genome. Although mobile genetic elements can only be identified as such if their mobility can be demonstrated in existing populations, transposon and transposon-like elements share several common biochemical and structural features. Here we demonstrate that a repetitive human sequence has many of the diagnostic features of transposable elements. This 2.3-kilobase (kb) transposon-like element contains two flanking long terminal repeat (LTR)-like 350-base pair (bp) repetitive sequences, each of which begins with the sequence 5' TG... and ends with ...CA 3'. The transposon-like element is bounded by 5-bp direct repeats. Discrete-length polyadenylated transcripts from HeLa cells are homologous to the transposon-like element. Members of this transposon-like family are found in extrachromosomal circular DNA molecules.

Animals↗
PubMed2004

Mutational analysis of the N-terminal DNA-binding domain of sleeping beauty transposase: critical residues for DNA binding and hyperactivity in mammalian cells.

The N-terminal domain of the Sleeping Beauty (SB) transposase mediates transposon DNA binding, subunit multimerization, and nuclear translocation in vertebrate cells. For this report, we studied the relative contributions of 95 different residues within this multifunctional domain by large-scale mutational analysis. We found that each of four amino acids (leucine 25, arginine 36, isoleucine 42, and glycine 59) contributes to DNA binding in the context of the N-terminal 123 amino acids of SB transposase, as indicated by electrophoretic mobility shift analysis, and to functional activity of the full-length transposase, as determined by a quantitative HeLa cell-based transposition assay. Moreover, we show that amino acid substitutions within either the putative oligomerization domain (L11A, L18A, L25A, and L32A) or the nuclear localization signal (K104A and R105A) severely impair its ability to mediate DNA transposition in mammalian cells. In contrast, each of 10 single amino acid changes within the bipartite DNA-binding domain is shown to greatly enhance SB's transpositional activity in mammalian cells. These hyperactive mutations functioned synergistically when combined and are shown to significantly improve transposase affinity for transposon end sequences. Finally, we show that enhanced DNA-binding activity results in improved cleavage kinetics, increased SB element mobilization from host cell chromosomes, and dramatically improved gene transfer capabilities of SB in vivo in mice. These studies provide important insights into vertebrate transposon biology and indicate that Sleeping Beauty can be readily improved for enhanced genetic research applications in mammals.

Amino Acid Sequence↗
PubMed2003

Divergence and transcriptional analysis of the division cell wall (dcw) gene cluster in Neisseria spp.

Three of the 18 open reading frames in the division and cell wall synthesis cluster of the pathogenic Neisseria spp. are not present in the clusters of other bacterial species. The region containing two of these, dcaB and dcaC, displays interstrain and interspecies variability uncharacteristic of such clusters. 3' of dcaB is a Correia repeat enclosed element (CREE), which is only present in some strains. It has been suggested that this CREE is a transcriptional terminator, although we demonstrate otherwise. A gearbox-like promoter within this CREE is active in Escherichia coli but not in Neisseria meningitidis. There is an active promoter 5' of dcaC, although its sequence is not conserved. The presence of similarly located promoters has not been demonstrated in other species. In Neisseria lactamica, this promoter involves another dcw-associated CREE, the first demonstration of active promoter generation at the 5' end of this common intergenic, apparently mobile, element. Upstream of this promoter is an inverted pair of neisserial uptake signal sequences, which are commonly considered to be transcriptional terminators. It has been proposed to terminate transcription in this location, although we have demonstrated transcript extending through this uptake signal sequence. dcaC contains a 108 bp tandem repeat, which is present in different copy numbers in the neisserial strains examined. This investigation reveals extensive sequence variation, disputes the presence of transcriptional terminators and identifies active internal promoters in this normally highly conserved cluster of essential genes, and addresses the transcriptional activity of two common neisserial intergenic components.

Bacterial Proteins↗
PubMed1986

Hybrid dysgenesis-induced revertants of insertions at the 5' end of the rudimentary gene in Drosophila melanogaster: transposon-induced control mutations.

Mutations in the 5' control region of the rudimentary (r) gene of Drosophila melanogaster were generated by using hybrid dysgenesis to mobilize P elements that were already inserted within this region. Eighteen new mutations out of 7793 chromosomes were isolated. Among the mutations were small insertions, deletions and inversions. All five of the deletions deleted into the 5' coding region of the r gene resulting in a severe mutant phenotype. The inversions and small insertions left the coding region intact, but altered the 5' control region. Northern analyses of the message levels in adult females indicated that these mutations alter the amount of the wild-type rudimentary message. These data also indicated that there is a region about 800 bp upstream of the start of transcription which is necessary for normal r expression. This region is not involved with the temporal and spatial regulation of r gene expression, but with the quantitative expression. An analysis of the DNA changes associated with each of the mutations demonstrates that P elements usually mobilize in an imprecise manner. Of the 22 mutations that have been isolated to date, only three are precise excisions. This means that P elements are potent mutators of the genome.

Animals↗
PubMed2003

Genetic variability of the frameshift region in IS911 transposable elements from Escherichia coli clinical isolates.

The IS911 bacterial transposable element has been analyzed for its mechanism of transposition and for the way it controls the expression of its genes by programmed -1 translational frameshifting. In the present study the prevalence of IS911 has been determined in the Enterobacteriaceae family and in other Gram-negative bacilli. Three variants, found in Escherichia coli clinical isolates and having mutations in the region implicated in frameshifting, were functionally characterized. All three were altered in their frameshifting and transposition abilities, suggesting that the frameshift region of IS911 may constitute a target for mutations reducing the transposition frequency of this mobile element in natural populations of E. coli.

DNA Transposable Elements↗
PubMed1997

Hybrid origin of a B chromosome (PSR) in the parasitic wasp Nasonia vitripennis.

Little is known about the origin and evolution of supernumerary (B) chromosomes. This study utilizes molecular markers to examine the evolutionary history and microstructural organization of the supernumerary paternal-sex-ratio (PSR) chromosome of the parasitic wasp Nasonia vitripennis. Copies of the retrotransposon NATE were previously isolated from PSR and the genomes of N. vitripennis and related wasp species. A phylogenetic analysis of sequences representing 29 elements from PSR and seven wasp species, coupled with a hybridization analysis of elements in genomic DNA provides evidence that PSR was recently transferred into N. vitripennis from a species in the genus Trichomalopsis. A linear region of the PSR chromosome was compared by Southern blot analysis with genomic DNA from N. vitripennis, Nasonia longicornis, Trichomalopsis americanus, and Trichomalopsis dubius. A region organized similarly to the region on PSR was not evident in any of the species, thus a progenitor region was not identified. However, the hybridizations revealed that this region of PSR is primarily composed of repetitive sequences that appear dispersed in these wasp genomes, and might represent additional mobile elements. At least three different dispersed repeats are present in the 18 kb region of PSR. The abundance of tandem and dispersed repetitive sequences in this relatively small region provides additional evidence for the degenerate structure of the PSR chromosome.

Animals↗
PubMed2004

The role of RNA polymerase sigma subunit in promoter-independent initiation of transcription.

In bacteria, initiation of transcription depends on the RNA polymerase sigma subunit, which brings catalytically proficient RNA polymerase core to promoters by binding to specific DNA elements located upstream of the transcription start point. Here, we study sigma-dependent synthesis of a transcript that is used to prime replication of the single-stranded genome of bacteriophage M13. We show that, in this system, sigma plays no role in DNA recognition, which is accomplished solely through RNA polymerase core interaction with DNA downstream of the transcription start point. However, sigma is required for full-sized transcript synthesis by allowing RNA polymerase core to escape into productive elongation. RNA polymerase sigma may play a similar role during replication primer synthesis in other bacterial mobile elements whose life cycle involves a single-stranded DNA stage.

Base Sequence↗