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At least 307 records · Page 17Linked to original sources
PubMed2005

Characterization of the highly variable region surrounding the bla(CTX-M-9) gene in non-related Escherichia coli from Barcelona.

OBJECTIVES: The dispersion of a clone, a plasmid or a mobile element carrying the bla(CTX-M-9) gene was evaluated in 30 Escherichia coli strains isolated in Barcelona between 1996 and 1999. The presence of the previously described orf513-bearing class 1 integron, In60, carrying the bla(CTX-M-9) gene, was also studied. METHODS: The clonality was analysed by pulsed-field gel electrophoresis. Plasmid analysis was performed by S1 digestion and hybridization with the CTX-M-9 probe. PCR mapping using specific designed primers was used to study the presence of In60 and In60-like structures. RESULTS: The clonality between the 30 strains was minor. The size of bla(CTX-M-9) carrying plasmids ranged between approximately 80 and 430 kb. One strain produced only a chromosome-encoded CTX-M-9 beta-lactamase. Thirty-six per cent of the strains showed differences with respect to the In60 structure due to an insertion or deletion events. CONCLUSIONS: These findings suggest that the bla(CTX-M-9) gene may be carried by a mobile element that disperses it between plasmids. The fast dispersion of the CTX-M-9 enzyme could therefore be due to both diffusion of plasmids and mobile elements.

Base Sequence↗
PubMed2003

The mosaic structure of the symbiotic plasmid of Rhizobium etli CFN42 and its relation to other symbiotic genome compartments.

BACKGROUND: Symbiotic bacteria known as rhizobia interact with the roots of legumes and induce the formation of nitrogen-fixing nodules. In rhizobia, essential genes for symbiosis are compartmentalized either in symbiotic plasmids or in chromosomal symbiotic islands. To understand the structure and evolution of the symbiotic genome compartments (SGCs), it is necessary to analyze their common genetic content and organization as well as to study their differences. To date, five SGCs belonging to distinct species of rhizobia have been entirely sequenced. We report the complete sequence of the symbiotic plasmid of Rhizobium etli CFN42, a microsymbiont of beans, and a comparison with other SGC sequences available. RESULTS: The symbiotic plasmid is a circular molecule of 371,255 base-pairs containing 359 coding sequences. Nodulation and nitrogen-fixation genes common to other rhizobia are clustered in a region of 125 kilobases. Numerous sequences related to mobile elements are scattered throughout. In some cases the mobile elements flank blocks of functionally related sequences, thereby suggesting a role in transposition. The plasmid contains 12 reiterated DNA families that are likely to participate in genomic rearrangements. Comparisons between this plasmid and complete rhizobial genomes and symbiotic compartments already sequenced show a general lack of synteny and colinearity, with the exception of some transcriptional units. There are only 20 symbiotic genes that are shared by all SGCs. CONCLUSIONS: Our data support the notion that the symbiotic compartments of rhizobia genomes are mosaic structures that have been frequently tailored by recombination, horizontal transfer and transposition.

Anaerobiosis↗
PubMed1994

LINE-related elements in Drosophila melanogaster.

Mobile elements known as LINEs are members of a superfamily of repeated DNA conserved from protozoa to man. These sequences propagate by the retrotranscription of RNA intermediates and differ in many respects from retroviruses. Whereas most eukaryotic genomes host a single LINE family, several families of LINE-like sequences or type II retrotransposons coexist in the fruit fly Drosophila melanogaster. Properties and features of these elements are discussed in this work.

Amino Acid Sequence↗
PubMed1999

Prediction of the impact of the Aznalcóllar toxic spill on the trace element contamination of agricultural soils.

The interaction of several trace elements (Cd, Zn, Cu, Pb, As, Bi, and Tl) was studied by leaching experiments in agricultural soils affected by the Aznalcóllar toxic spill. The spill led to contamination by acid waste waters and sludge deposition. The levels of contamination recorded after the sludge was removed from soils showed that highly contaminated areas remained. A comparison of soils directly affected by sludge deposition and acid waste waters with soils contaminated only by acid waste waters demonstrated that Zn/As and Cd/As ratios were good indicators of the two contributions to the contamination. Soil samples were characterised and grouped according to their texture and carbonate content. The response of elements to single extractions with CaCl2 0.01 mol l-1, CaCl2 1 mol l-1, CH3COOH 0.43 mol l-1, and EDTA 0.05 mol l-1 enabled us to estimate their mobility in the soils. Cd and Zn were found to be the most mobile elements. Cu showed an intermediate mobility, especially in an acidic medium. Pb, As, Bi and Tl were found to be non-mobile elements. A comparison of referent, low and highly contaminated samples showed that the presence of sludge had an effect on desorption yields, in part due to the short-term after the contamination. Calculations of a relative scale of long-term mobility, between soils and trace elements, provided further conclusions derived from the use of single extractions.

Accidents, Occupational↗
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↗
PubMed1993

Lateral transfer in natural populations of eukaryotes.

Although there are several likely instances of trans-kingdom lateral transfer of genomic sequences involving eukaryotes and prokaryotes, almost all well-documented cases of eukaryote to eukaryote transfer seem to involve mobile elements or other parasitic sequences. Consistent with general observations of phylogenetic regularity, the limited molecular evidence suggests that lateral transfer of eukaryotic genomic sequences is at best very rare. However, due to limited data, the possibility of rare transfers that could have considerable evolutionary significance cannot be ruled out. A possible propensity for lateral transfer by mobile elements may reflect their innate capacity for genomic wandering. In addition, occasional cross-species mobility may play a critical role in the long-term evolutionary survival of these elements and have been subject to natural selection. Much work is needed to fully understand the dynamics of TEs and other multigene families. Problems of paralogy, recombination, and variation in evolutionary rates currently present important difficulties in distinguishing conclusively between occasional lateral transfer and strictly vertical transfer. The importance of lateral transfers for host organisms must await answers to more general questions about the long-term evolutionary significance of mobile elements and the extent to which they can act as vectors for host genomic sequences.

Animals↗
PubMed1991

Environmental stresses and mobilization of transposable elements in inbred lines of Drosophila melanogaster.

Drastic changes in insertion patterns of the mobile elements copia and mdg-1 (a copia-like element) were checked in highly inbred lines of Drosophila melanogaster subjected to various stresses. Flies were treated by factors known for their ability to increase mutation rates of classical genes, and for their action on transcription or transposition of mobile elements: heat shocks at 37 degrees C, dichlorvos, hydrogen peroxide and ecdysterone. The insertion patterns were analyzed in progenies of the treated flies, either on larvae by in situ hybridization of giant salivary gland chromosomes, or on adult flies by Southern blotting interpreted by densitometric analysis. The techniques used made it possible to detect only changes with frequencies of more than 10% of the insertion sites. We show that the copia and mdg-1 elements cannot be radically mobilized in our inbred lines under the stressful conditions used. This absence of 'explosion' of mobilization of transposable elements after the action of external factors suggests that the genomes of our highly inbred lines are relatively protected against environmental stresses.

Animals↗
PubMed2002

P element-mediated duplications of genomic regions in Drosophila melanogaster.

Previously we have described highly unstable yellow mutations induced by chimeric elements that consist of genomic sequences originating from different regions of the X chromosome flanked by identical copies of an internally deleted 1.2 kb P element. To study further the origin and the mechanism of formation of chimeric mobile elements, we analyzed complex y-sc mutations, induced by inversions between P elements located in the neighboring yellow and scute loci. The breakpoints of the inversions are flanked by two P elements in head-to-head orientation on one side and by one P element on the other side. Such an arrangement of P elements leads to frequent duplication into the site between the two P element copies located in head-to-head orientation of the yellow sequences adjacent to the single P element. The duplicated yellow sequences either partly replace the sequence of one of the P elements or are inserted between the conserved head-to-head oriented P elements. In some cases two copies of the yellow sequence are duplicated between the P elements in inverted tail-to-tail orientation. The structure of the P elements at the place of duplication and of the P element- yellow junction suggests that the described duplications, which form chimeric mobile elements, are generated through the previously proposed synthesis-dependent strand annealing mechanism.

Animals↗
PubMed2003

Mobile genetic elements and bacterial toxinoses: the superantigen-encoding pathogenicity islands of Staphylococcus aureus.

It is a remarkable observation that virtually all bacterial toxins associated with specific clinical conditions (toxinoses) are encoded by mobile (and therefore variable) genetic elements. Remarkably, these rarely, if ever, carry determinants of antibiotic resistance. Examples are the toxins responsible for diphtheria, anthrax, tetanus, botulism, cholera, toxic shock, scarlet fever, exfoliative dermatitis, food poisoning, travelers' diarrhea, shigella dysentery, necrotizing pneumonia, and others. A recently discovered example of this phenomenon is the family of related staphylococcal pathogenicity islands encoding superantigens (SAgs). These are 15-20kb elements that occupy constant positions in the chromosomes of toxigenic strains, and are characterized by certain phage-related features, namely genes encoding integrases, helicases, and terminases, and the presence of flanking direct repeats. The prototype, SaPI1 of Staphylococcus aureus, encodes TSST-1 plus two newly described SAgs, SEK and SEL. Other members of the family encode enterotoxins B (SaPI3) and C (SaPI4), plus at least two other SAgs each. SaPI1 and SaPI2, also encoding TSST-1, are excised and induced to replicate by certain staphylococcal phages, and are then encapsidated at high efficiency into phage-like infectious particles with heads about 1/3 the size of the helper phage heads, commensurate with the sizes of the respective genomes. This results in transfer frequencies of the order of 10(8)/ml, and is presumably responsible for the spread of these elements as well as for their acquisition in the first place. In the absence of a helper phage, these two islands are highly stable; neither excision, loss, or transfer occurs at detectable frequency. Several general implications of this phenomenon will be discussed. One is that the determinants of these toxins have been imported from other species and therefore are not components of the basic genome of the extant producing organisms. This raises the question of the biological (adaptive?) roles of these toxins. Another is that the toxin-carrying units can spread among different (though probably related) species. An interesting question is that of the biological basis for the separation of toxin and resistance determinants.

Animals↗
PubMed2026

Satellite DNA evolution in Tytonidae (Aves: Strigiformes): dynamic repeat landscapes despite conserved karyotypes.

The elevated chromosome numbers observed in Tytonidae relative to the putative ancestral avian karyotype suggest that lineage-specific chromosomal fissions may have played an important role in the evolutionary history of this family. Here, we provide the first cytogenetic characterization of the American barn owl (Tyto furcata) and performs a comparative repeatome analysis across members of the Tytonidae, including other two species, the Western barn owl (Tyto alba), and the Oriental bay owl (Phodilus badius). The karyotype of T. furcata showed a 2n = 92, closely resembling that previously described for T. alba, indicating a high degree of chromosomal conservation within Tytonidae. Although T. furcata and T. alba exhibit similar karyotypic organization, comparative repeatomic analyses revealed differences in their composition, including variation in satellite DNA (satDNA) repertoires and abundance. Eight satDNA families were identified in T. furcata, nine in T. alba, and 28 in P. badius, highlighting the dynamic evolution of repetitive sequences. Several satDNA families were shared between T. furcata and T. alba, whereas some appeared species-specific, supporting the library hypothesis of satDNA evolution. In P. badius, multiple satDNAs exhibited similarity to transposable elements, suggesting that mobile elements contributed to their diversification. Cytogenetic analyses demonstrated centromeric heterochromatin distribution in T. furcata, as well as a large heterochromatic W chromosome enriched in DNA repeats. The localization of satDNAs in centromeric regions and the apparent accumulation of repeats on the W chromosome reinforce the role of repetitive sequences in chromosome organization and sex chromosome differentiation. Together, these findings reveal repeatome diversification despite conserved macrochromosomal structure and provide new insights into genome evolution and chromosomal dynamics in birds.

Animals↗
PubMed1987

Trypanosoma brucei repeated element with unusual structural and transcriptional properties.

The genome of Trypanosoma brucei contains up to 400 copies of a conserved sequence (TRS, trypanosome repeated sequence). The majority of TRS copies (TRS1) are 5.2 X 10(3) base-pairs (kb) and are flanked by different separate halves of the previously described transposable element RIME (ribosomal mobile element), although a variant copy (TRS2) contains only the central 1.45 kb portion and lacks RIME. TRS1 elements can probably undergo transposition, since they are dispersed in all chromosome size classes and are bordered by direct repeats of about four base-pairs. Some TRS1 elements may contain an open reading frame over almost their entire length (1651 codons), encoding a protein showing homology with reverse transcriptase. TRS probes detect poly(A)+ transcripts of 5 to 9 kb, generated by a polymerase moderately sensitive to alpha-amanitin. Transcription is developmentally regulated. Both TRS and RIME sense transcripts are preferentially synthesized compared to anti-sense transcripts, and are much more abundant in bloodstream forms than in cultured procyclics.

Animals↗
PubMed2005

Xylella and Xanthomonas Mobil'omics.

The gamma-proteobacterium Xanthomonadales groups two closely related genera of plant pathogens, Xanthomonas and Xylella. Whole genome sequencing and comparative analyses disclosed a high degree of identity and co-linearity of the chromosome backbone between species and strains. Differences observed are usually clustered into genomic islands, most of which are delimited by genetic mobile elements. Focus is given in this paper to describe which groups of mobile elements are found and what is the relative contribution of these elements to Xanthomonas and Xylella genomes. Insertion sequence (IS) elements have invaded the Xanthomonas genome several times, whereas Xylella is rich in phage-related regions. Also, different plasmids are found inhabiting the bacterial cells studied here. Altogether, these results suggest that the integrative elements such as phages and transposable elements as well as the episomal plasmids are important drivers of the genome evolution of this important group of plant pathogens.

Amino Acid Sequence↗
PubMed1999

A novel tripartite structure comprising a mariner-like element and two additional retrotransposons found in the Bombyx mori genome.

A clone of a DNA-mediated mobile element (transposon) corresponding to a mariner-like element (MLE) was obtained by carrying out the polymerase chain reaction with genomic DNA of Bombyx mori using a Hyalophora cecropia MLE sequence as a primer. This clone had a size of about 4.2 kb and, after sequencing, was found to contain an RNA-mediated, shorter retrotransposon named L1Bm, which was in turn integrated with a much longer retrotransposon named BMC1. Thus, the mobile elements made a novel tripartite structure. The BMC1 and L1Bm moieties of the composite structure each contained a 63-bp conserved sequence which was subsequently found to be highly conserved in all BMC1 and L1Bm elements registered so far. We propose that the 63-bp stretch may be a recognition site for a retrotransposition mechanism conducted by a reverse transcriptase and an endonuclease complex. On the basis of this inference, we propose a model that predicts how different types of BMC1 and L1Bm elements are dispersed in the genome. In addition, a phylogenetic tree made from the current and extant BMC1 and L1Bm sequences indicated that these elements can be classified into Subfamilies I and II.

Animals↗
PubMed2005

Live imaging of bidirectional traffic from the ERGIC.

The endoplasmic reticulum-Golgi intermediate compartment (ERGIC) defined by the cycling lectin ERGIC-53 consists of tubulovesicular clusters, but it is unknown if these membranes are transport vehicles or stationary entities. Here, we show by live imaging that GFP-ERGIC-53 mainly localizes to long-lived stationary and some short-lived highly mobile elements. Unlike the anterograde marker VSV-G-GFP, GFP-ERGIC-53 does not vectorially move to the Golgi upon exit from the ERGIC, as assessed by a novel quantitative vector field method. Dual-color imaging of GFP-ERGIC-53 and a secretory protein (signal-sequence-tagged dsRed) reveals that the stationary elements are sites of repeated sorting of retrograde and anterograde cargo, and are interconnected by highly mobile elements. These results suggest that the ERGIC is stationary and not simply a collection of mobile carriers that mediate protein traffic from endoplasmic reticulum to Golgi.

Biological Transport, Active↗
PubMed1989

The beta heterochromatic sequences flanking the I elements are themselves defective transposable elements.

Phylogenetic studies suggest that mobile element families are unstable components of the Drosophila genome. Two examples of immobilization of a transposable element family are presented here: as judged by their constant genomic organization among unrelated strains, the F and I element families have been respectively immobilized for a long time in D. simulans and in the reactive D. melanogaster strains (these are the laboratory strains which escaped the recent I invasion of D. melanogaster natural populations). All the elements of these defective families are located in the beta heterochromatic portion of the genome. Moreover, most if not all of the beta heterochromatic sequences into which the defective I elements are embedded are themselves non-mobile members of various nomadic families such as mdg 4, 297, 1731, F and Doc. These results are discussed with special emphasis on the possible nomadic origin of beta heterochromatin components and on the mechanisms of evolutionary turnover of the transposable element families.

Animals↗
PubMed1999

S1 SINE retroposons are methylated at symmetrical and non-symmetrical positions in Brassica napus: identification of a preferred target site for asymmetrical methylation.

DNA methylation has been often proposed to operate as a genome defence system against parasitic mobile elements. To test this possibility, the methylation status of a class of plant mobile elements, the S1Bn SINEs, was analysed in detail using the bisulfite modification method. We observed that S1Bn SINE retroposons are methylated at symmetrical and asymmetrical positions. Methylated cytosines are not limited to transcriptionally important regions but are well distributed along the sequence. S1Bn SINE retroposons are two-fold more methylated than the average methylation level of the Brassica napus nuclear DNA. By in situ hybridization, we showed that this high level of methylation does not result from the association of S1Bn elements to genomic regions known to be highly methylated suggesting that S1Bn elements were specifically methylated. A detailed analysis of the methylation context showed that S1Bn cytosines in symmetrical CpG and CpNpG sites are methylated at a level of 87% and 44% respectively. We observed that 5.3% of S1Bn cytosines in non-symmetrical positions were also methylated. Of this asymmetrical methylation, 57% occurred at a precise motif (Cp(A/T)pA) that only represented 12% of the asymmetrical sites in S1Bn sequences suggesting that it represents a preferred asymmetrical methylation site. This motif is methylated in S1Bn elements at only half the level observed for the Cp(A/T)pG sites. We show that non-S1Bn CpTpA sites can also be methylated in DNA from B. napus and from other plant species.

5-Methylcytosine↗
PubMed1998

A novel Alu-like element rearranged in the dystrophin gene causes a splicing mutation in a family with X-linked dilated cardiomyopathy.

We have identified and characterized a genomic sequence with some features typical of Alu-like mobile elements rearranged into the dystrophin gene in a family affected by X-linked dilated cardiomyopathy. The Alu-like sequence rearrangement occurred 2.4 kb downstream from the 5' end of intron 11 of the dystrophin gene. This rearrangement activated one cryptic splice site in intron 11 and produced an alternative transcript containing the Alu-like sequence and part of the adjacent intron 11, spliced between exons 11 and 12. Translation of this alternative transcript is truncated because of the numerous stop codons present in every frame of the Alu-like sequence. Only the mutant mRNA was detected in the heart muscle, but in the skeletal muscle it coexisted with the normal one. This result is supported by the immunocytochemical findings, which failed to detect dystrophin in the patient's cardiac muscle but showed expression of a reduced level of protein in the skeletal muscle. Comparative analysis of the Alu-like sequence showed high homology with other repeated-element-containing regions and with several expressed sequence tags. We suggest that this Alu-like sequence could represent a novel class of repetitive elements, reiterated and clustered with some known mobile elements and capable of transposition. Our report underlines the complexity of the pathogenic mechanism leading to X-linked dilated cardiomyopathy but suggests that differences in tissue-specific expression of dystrophin mutations may be a common feature in this condition.

Adult↗
PubMed1997

Homing of a group II intron from Lactococcus lactis subsp. lactis ML3.

Ll.ltrB is a functional group II intron located within a gene (ltrB) encoding a conjugative relaxase essential for transfer of the lactococcal element pRSO1. In this work, the Ll.ltrB intron was shown to be an independent mobile element capable of inserting into an intronless allele of the ltrB gene. Ll.ltrB was not observed to insert into a deletion derivative of the ltrB gene in which the intron splice site was removed. In contrast, a second vector containing a 271-nucleotide segment of ltrB spanning the Ll.ltrB splice site was shown to be a proficient recipient of intron insertion. Efficient homing was observed in the absence of a functional host homologous recombination system. This work demonstrates that the Ll.ltrB intron is a novel site-specific mobile element in lactococci and that group II intron self-transfer is a mechanism for intron dissemination among bacteria.

Alleles↗