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PubMed1990

Transposition rates of movable genetic elements in Drosophila melanogaster.

A considerable proportion of visible mutations is reported to be caused by the insertion of mobile genetic elements in Drosophila and other organisms. We estimated transposition rates of some Drosophila mobile elements by using the lines AW and JH in which spontaneous mutations have been accumulated independently for about 400 generations. Occupied sites of the mobile elements were detected by in situ hybridization on the salivary gland chromosomes sampled from 40 AW and 30 JH lines. The rates of insertion and excision of the copia and two copia-like elements, 412 and 17.6, are very low: Insertions occurred at up to 10(-3) per second chromosome per generation (17.6) and excision occurred at about 10(-5) per site per generation (copia and 412). Insertions of the I and hobo elements occurred much more frequently. These estimates are not only important for assessing the actual rate of various types of mutations but also for developing an evolutionary theory of mobile elements themselves.

Animals↗
PubMed2005

Woody biomass phytoremediation of contaminated brownfield land.

Economic and environmental regeneration of post-industrial landscapes frequently involves some element of re-afforestation or tree planting. We report field trials that evaluate whether woody biomass production is compatible with managing residual trace element contamination in brownfield soils. Large-scale mapping of contamination showed a heterogenous dispersion of metals and arsenic, and highly localised within-site hotspots. Yields of Salix, Populus and Alnus were economically viable, showing that short-rotation coppice has a potentially valuable role in community forestry. Mass balance modelling demonstrated that phytoextraction potentially could reduce contamination hotspots of more mobile elements (Cd and Zn) within a 25-30-year life cycle of the crops. Cd and Zn in stems and foliage of Salix were 4-13 times higher than EDTA-extractable soil concentrations. Lability of other trace elements (As, Pb, Cu, Ni) was not increased 3 years after planting the coppice; woody biomass may provide an effective reduction of exposure (phyto-stabilization) to these less mobile contaminants.

Alnus↗
PubMed2001

A family of DNA repeats in Aspergillus nidulans has assimilated degenerated retrotransposons.

In the course of a chromosomal walk towards the centromere of chromosome IV of Aspergillus nidulans, several cross-hybridizing genomic cosmid clones were isolated. Restriction mapping of two such clones revealed that their restriction patterns were similar in a region of at least 15 kb, indicating the presence of a large repeat. The nature of the repeat was further investigated by sequencing and Southern analysis. The study revealed a family of long dispersed repeats with a high degree of sequence similarity. The number and location of the repeats vary between wild isolates. Two copies of the repeat contained degenerated long-terminal-repeat (LTR) retrotransposons, which were named Dane1 and Dane2 (for Degenerated Aspergillus nidulans element). The pattern of degeneration suggested that a process similar to the repeat-induced point-mutation (RIP) phenomenon, first described in Neurospora crassa, may have operated in A. nidulans. The data indicate that this family of repeats has assimilated mobile elements that subsequently degenerated but then underwent further duplications as a part of the host repeats.

Amino Acid Sequence↗
PubMed1997

The Clostridium perfringens enterotoxin gene is on a transposable element in type A human food poisoning strains.

The Clostridium perfringens enterotoxin gene (cpe) is rarely found in naturally isolated strains. In human food poisoning strains, cpe is found on the chromosome, and is located episomally in animal isolates. Observations that the gene was somewhat unstable and could be gained or lost suggested that the gene was on a mobile element. An IS200-like element, IS1469, is almost always upstream of cpe. A new insertion element was identified, IS1470, a member of the IS30 family, which is found both up-an downstream of cpe in the type A strain NCTC 8239. PCR results confirmed that this configuration was conserved in type A human food poisoning strains. The enterotoxin gene was on a 6.3 kb transposon which, in addition to the two flanking copies of IS1470, included IS1469 and two 1 kb stretches, one on each side of cpe, with no open reading frames. Results indicated that 14 bp was copied from the genome during insertion. Details of the configuration of DNA in this transposon are presented, and the possible connection of this transposon with the movement of the enterotoxin gene is discussed.

Animals↗
PubMed1991

P element excision in Drosophila melanogaster and related drosophilids.

The frequency of P element excision and the structure of the resulting excision products were determined in three drosophilid species. Drosophila melanogaster, D. virilis, and Chymomyza procnemis. A transient P element mobility assay was conducted in the cells of developing insect embryos, but unlike previous assays, this mobility assay permitted the recovery of excision products from plasmids regardless of whether the excision event was precise or imprecise. Both quantitative and qualitative differences between the products of excision in the various species studied were observed. The frequency with which P element excision products were recovered from D. melanogaster was 10-fold greater than from D. virilis and C. procnemis; however, the proportion of all excision events resulting in the reversion of a P-induced mutant phenotype was the same. Virtually all excision products recovered, including those resulting in a reversion of the mutant phenotype, did not result in the exact restoration of the original target sequence. Sequence analysis suggested that duplex cleavage at the 3' and 5' termini of the P element, or their subsequent modification, occurred asymmetrically and interdependently. P element-encoded transposase was not absolutely required for P element excision.

Animals↗
PubMed1997

Transposable elements as sources of variation in animals and plants.

A tremendous wealth of data is accumulating on the variety and distribution of transposable elements (TEs) in natural populations. There is little doubt that TEs provide new genetic variation on a scale, and with a degree of sophistication, previously unimagined. There are many examples of mutations and other types of genetic variation associated with the activity of mobile elements. Mutant phenotypes range from subtle changes in tissue specificity to dramatic alterations in the development and organization of tissues and organs. Such changes can occur because of insertions in coding regions, but the more sophisticated TE-mediated changes are more often the result of insertions into 5' flanking regions and introns. Here, TE-induced variation is viewed from three evolutionary perspectives that are not mutually exclusive. First, variation resulting from the intrinsic parasitic nature of TE activity is examined. Second, we describe possible coadaptations between elements and their hosts that appear to have evolved because of selection to reduce the deleterious effects of new insertions on host fitness. Finally, some possible cases are explored in which the capacity of TEs to generate variation has been exploited by their hosts. The number of well documented cases in which element sequences appear to confer useful traits on the host, although small, is growing rapidly.

Adaptation, Physiological↗
PubMed1997

Statistical modeling and analysis of the LAGLIDADG family of site-specific endonucleases and identification of an intein that encodes a site-specific endonuclease of the HNH family.

The LAGLIDADG and HNH families of site-specific DNA endonucleases encoded by viruses, bacteriophages as well as archaeal, eucaryotic nuclear and organellar genomes are characterized by the sequence motifs 'LAGLIDADG' and 'HNH', respectively. These endonucleases have been shown to occur in different environments: LAGLIDADG endonucleases are found in inteins, archaeal and group I introns and as free standing open reading frames (ORFs); HNH endonucleases occur in group I and group II introns and as ORFs. Here, statistical models (hidden Markov models, HMMs) that encompass both the conserved motifs and more variable regions of these families have been created and employed to characterize known and potential new family members. A number of new, putative LAGLIDADG and HNH endonucleases have been identified including an intein-encoded HNH sequence. Analysis of an HMM-generated multiple alignment of 130 LAGLIDADG family members and the three-dimensional structure of the I- Cre I endonuclease has enabled definition of the core elements of the repeated domain (approximately 90 residues) that is present in this family of proteins. A conserved negatively charged residue is proposed to be involved in catalysis. Phylogenetic analysis of the two families indicates a lack of exchange of endonucleases between different mobile elements (environments) and between hosts from different phylogenetic kingdoms. However, there does appear to have been considerable exchange of endonuclease domains amongst elements of the same type. Such events are suggested to be important for the formation of elements of new specficity.

Amino Acid Sequence↗
PubMed2001

Embolism from the Aorta: Atheroemboli and Thromboemboli.

To date, there are no evidence-based data to support specific drug therapy for a patient with atheroembolism. It makes sense to use HMG CoA (3-hydroxy-3-methylglutaryl coenzyme A) reductase inhibitors (statins) in any patient with atherosclerosis, as these drugs have been shown to reduce the risk of myocardial infarction and stroke, and have a theoretical benefit on plaque stabilization. Surgical treatment should be considered for patients with abdominal aortic or popliteal artery aneurysms and downstream atheroembolism. There are case reports of atheroemboli in patients worsening after given warfarin or heparin. For this reason, some institutions are reluctant to prescribe these drugs for patients with atheroemboli or thromboemboli from aortic plaque. However, the incidence of this complication is quite low. Anticoagulation probably should be stopped if a patient develops atheroembolism. Similarly, the current state of knowledge does not allow for selecting specific pharmacologic intervention in patients with thromboemboli from aortic plaque. Statin therapy does make sense, as these drugs theoretically stabilize plaques and prevent plaque hemorrhage, thrombosis, and subsequent embolization. Unstable aortic plaques may develop superimposed thrombi (red thrombi on pathologic examination), easily seen as mobile elements on transesophageal echocardiography. Therefore, it is possible that anticoagulation with warfarin might prevent embolic events in these patients. For this reason, we are often in the position of recommending warfarin therapy for patients with emboli and severe atheromas seen on transesophageal echocardiography, especially when superimposed mobile thrombi are seen. There are small series in the literature that indicate the potential benefit of warfarin. However, until a large multicenter randomized clinical trial is done, the use of warfarin can not be definitively recommended. Antiplatelet agents, although safer than warfarin (less risk of hemorrhage), have not been proven beneficial in patients with thromboembolism from the aorta. Surgery (endarterectomy) of the aortic arch is a very risky procedure that should not be performed routinely, but may be used in highly selected patients.

Journal Article↗
PubMed2026

Novel bacterial hosts and mobile genetic structure of tet(X) variants in tetracycline-contaminated aquatic environment uncovered by culture and long-read metagenomics.

Clinically important tigecycline (3rd-generation tetracycline) resistance tet(X) variants were inferred to have evolutionarily originated from environmental bacteria, and have been recognized among environment, human and animals. However, genetic basis for environmental proliferation and dissemination of tet(X) variants remains ambiguous. This study profiled tet(X) variants at gene, contig, isolate, and community levels in environmental community subjected to long-term stepwise increasing oxytetracycline (1st-generation tetracycline) or tigecycline pressure using long-term microcosm experiments, quantitative PCR, bacterial isolation, whole-genome sequencing, and Nanopore-based long-read metagenomics. We confirmed that both oxytetracycline and tigecycline enriched the abundance of tetracycline resistance genes especially oxytetracycline-enriched tet(X3). Unexpectedly diverse bacterial hosts and genetic structure of tet(X)-positive mobile elements in the environment microbiome were identified using bacterial isolation and long-read Nanopore metagenomics. Pseudomonas defluvii was first reported to carry tet(X3) in the chromosome, forming IS26-tet(X3)-res-ISCR2 circular intermediate to transfer between different DNA molecules. Database mining revealed similar mobile segments have prevailed among animal-derived Acinetobacter species. Unlike the widely reported ISCR2-mediated transfer of tet(X6), we identified a novel mobile multidrug transposon TnAs3 where tet(X6) and class 1 integron co-transferred as its passenger region. Mobile tet(X2)-ere(D)-aadS-erm(F)-blaOXA-347 segment was annotated in Runella, and co-occurrences of tet(X2) and ere(D), aadS, blaOXA-347 were also found in Flavobacterium, Arsenicibacter, Chryseobacterium and Pedobacter. Overall, tetracycline-contaminated aquatic microbiome harboured diverse mobile tet(X)-positive segments which have not yet been acquired by clinical pathogens, and thus served as the genetic pool of tet(X) variants together with indigenous bacterial hosts, especially the newly reported Pseudomonas defluvii. Reducing pollution of older-generation tetracyclines would be a proactive way to mitigate environmental evolution and possible clinical effects of tet(X) variants.

Metagenomics↗
PubMed2006

Recoding in bacteriophages and bacterial IS elements.

Dynamic shifts between open reading frames and the redefinition of codon meaning at specific sites, programmed by signals in mRNA, permits versatility of gene expression. Such alterations are characteristic of organisms in all domains of life and serve a variety of functional purposes. In this article, we concentrate on programmed ribosomal frameshifting, stop codon read-through and transcriptional slippage in the decoding of phage genes and bacterial mobile elements. Together with their eukaryotic counterparts, the genes encoding these elements are the richest known source of nonstandard decoding. Recent analyses revealed several novel sequences encoding programmed alterations in gene decoding and provide a glimpse of the emerging picture.

Bacteriophages↗
PubMed1995

Human and other mammalian genomes contain transposons of the mariner family.

Internal fragments of the putative transposase gene of mariner-like elements (MLEs) were amplified from human, mouse, rat, chinese hamster, sheep and bovine genomic DNAs by polymerase chain reaction (PCR). The sequences identified in human, ovine and bovine genomes correspond to ancient degenerate transposons. Screening mammalian sequence libraries identified a truncated element in the human ABL gene and the sequence of its 5'-ITR was determined. This ITR sequences were used in PCR experiments with DNA from six mammalian species and detected full-sized and deleted MLEs. The presence of MLE in mammalian genomes demonstrates that they are ubiquitous mobile elements found from fungi to man. This observation strongly raises the possibility that MLE could constitute tools for the modification of eucaryotic genomes.

Amino Acid Sequence↗
PubMed2005

Straightening out the LINEs: LINE-1 orthologous loci.

The L1Hs preTa subfamily of long interspersed elements (LINEs) originated after the divergence of human and chimpanzee and is therefore found only in the human genome. Thirty-three of the 254 L1Hs preTa elements are polymorphic for the absence/presence of the insertion, making them useful markers for studying human population genetics. The problem of homoplasy, however, can diminish the value of LINEs as phylogenetic and population genetic markers. We examined anomalous orthologous sites in a range of nonhuman primates. Only two cases of other mobile elements inserting near the preintegration sites of L1Hs preTa elements were observed: an AluY insertion in Chlorocebus and an L1PA8 insertion in Aotus. Sequence analysis showed that both elements were clearly distinguishable from their human counterparts. We conclude that L1 elements can continue to be regarded as essentially homoplasy-free genetic characters.

Animals↗
PubMed1981

[Mobile dispersed genetic elements in eukaryotes and their possible relationship to carcinogenesis].

During last three years, the mobile dispersed genetic elements (mdg) were isolated from the genome of Drosophila melanogaster, yeasts and mammals. According to a number of their properties, mdg elements are quite similar to endogenous pro-retroviruses. It is known that in many cases oncogeneity of retroviruses depends on the incorporation of the certain host genes (potential oncogenes) into the viral genome. We suggest that in some cases mdg elements could entrap the potential oncogenes in the course of transposition. As a result, oncogenes become uncontrollable by host regulatory systems and may induce cell transformation. Another possible mechanism underlying switch off of the gene responsible for differentiation control may be mdg transposition to a region in close vicinity of the gene. As transposition of mdg elements seems to occur rather often, they may be regarded as one of the most important factors of genome rearrangements leading to cell transformation.

Animals↗
PubMed2000

The complete Tirant transposable element in Drosophila melanogaster shows a structural relationship with retrovirus-like retrotransposons.

We have determined the structure and organization of Tirant, a retrotransposon of Drosophila melanogaster reported in literature to be responsible for four independent mutations. Tirant is a long terminal repeat (LTR) retrotransposon 8527bp long. It possesses three open reading frames (ORF) encoding Gag, Pol and Env proteins with a strong similarity with ZAM, a recently identified member of the gypsy class of retrovirus-like mobile elements. Molecular analysis of the Tirant genomic copies present in four D. melanogaster strains revealed that most of them are defective, non-autonomous elements that differ in the position and extension of the conserved internal portion. Defective elements lacking the Gag ORF but retaining the Env ORF are abundant in heterochromatin. Four discrete Tirant transcripts are observed during embryogenesis in the strain Oregon-R, the smaller of which, 1.8kb in size, originates from the splicing of a primary transcript and leads to a subgenomic RNA coding for the Env product.

Amino Acid Sequence↗
PubMed2006

Isolation and characterization of functional insertion sequences of rhizobia.

Rhizobia are a group of bacteria that form nodules on the roots of legume host plants. The sequenced genomes of the rhizobia are characterized by the presence of many putative insertion sequences (IS) elements. However, it is unknown whether these IS elements are functional and it is therefore relevant to assess their transposition activity. In this work, several functional insertion sequences belonging to the IS1256, IS3, IS5, IS166, and IS21 families were captured from Rhizobium tropici, Rhizobium sp. NGR234 and Sinorhizobium meliloti, using pGBG1 as a trapping system. In silico analysis shows that homologs of rhizobia mobile elements are present in distantly related genomes, suggesting that Rhizobium IS elements are prone to genetic transfer.

Computational Biology↗
PubMed2005

The IncP-6 plasmid Rms149 consists of a small mobilizable backbone with multiple large insertions.

Plasmid Rms149, the archetype of Pseudomonas plasmid incompatibility group IncP-6, was identified in Pseudomonas aeruginosa as an agent conferring resistance to streptomycin, sulfanilamide, gentamicin, and carbenicillin in 1975. It has been classed as a broad-host-range plasmid due to its ability to replicate in both Escherichia coli (where it is designated IncG) and Pseudomonas species, although both species are gamma-proteobacteria. To provide reference information on this Inc group, we have determined the complete sequence of Rms149 and found that, although the genome comprises 57,121 bp, it is essentially a small mobilizable plasmid carrying multiple mobile elements, which make up 79% (>45 kb) of its genome. A replicon has been identified which encodes a single polypeptide with moderate identity to other replication proteins. The region encoding this protein can replicate in Pseudomonas putida and E. coli. This sequence is directly downstream of a putative partitioning region highly similar to that of pRA2. A functional IncQ-type mobilization region is also present. Thus, the backbone appears to be a novel combination of modules already identified in other plasmid systems. Analysis of the segments that fall outside this core of stable inheritance and transfer functions show that this plasmid has been subject to multiple insertion events and that the plasmid appears to carry a considerable load of DNA that no longer should be phenotypically advantageous. The plasmid therefore functions not just as a vehicle for spread of selective traits but also as a store for DNA that is not currently under selection.

Bacterial Proteins↗
PubMed1978

Studies on molybdenum absorption and transport in bean and rice.

The patterns of molybdenum (MoO(4) (2-)) absorption and transport were investigated in intact bean (Phaseolus vulgaris L.) and rice (Oryza sativa L. cv. I.R.8) plants. The mobility of MoO(4) (2-) absorbed by roots and by leaves was compared with that of a freely mobile element, Rb(+). Although MoO(4) (2-) absorption by bean roots was nearly as high as that of Rb(+), its transport to the shoot was considerably less. When MoO(4) (2-) was fed to one of the primary leaves, most of it was transported to the stem and root. Evidence obtained here showed that MoO(4) (2-) was mobile. Experiments with intact rice seedlings revealed large differences in the absorption and transport of MoO(4) (2-) between the plants grown in CaSO(4) and those in Hoagland solution. Molybdate uptake by excised rice roots was suggested to be an active process since it was greatly inhibited by a metabolic inhibitor. The presence of Mn(2+), Zn(2+), Cu(2+), CI(-), or SO(4) (2-) in the absorption medium reduced MoO(4) (2-) uptake which was markedly enhanced by the presence of Fe(2+).

Journal Article↗
PubMed2002

Shared protein components of SINE RNPs.

The heterogeneous, short RNAs produced from the high, copy, short mobile elements (SINEs) interact with proteins to form RNA-protein (RNP) complexes. In particular, the BC1 RNA, which is transcribed to high levels specifically in brain and testis from one locus of the ID SINE family, exists as a discrete RNP complex. We expressed a series of altered BC1, and other SINE-related RNAs, in several cell lines and tested for the mobility of the resulting RNP complexes in a native PAGE assay to determine which portions of these SINE RNAs contribute to protein binding. When different SINE RNAs were substituted for the BC1 ID sequence, the resulting RNPs exhibited the same mobility as BC1. This indicates that the protein(s) binding to the ID portion of BC1 is not sequence specific and may be more dependent upon the secondary structure of the RNA. It also suggests that all SINE RNAs may bind a similar set of cellular proteins. Deletion of the A-rich region of BC1 RNA has a marked effect on the mobility of the RNP. Rodent cell lines exhibit a slightly different mobility for this shifted complex when compared to human cell lines, reflecting evolutionary differences in one or more of the protein components. On the basis of mobility change observed in RNP complexes when the A-rich region is removed, we decided to examine poly(A) binding protein (PABP) as a candidate member of the RNP. An antibody against the C terminus of PABP is able to immunoprecipitate BC1 RNA, confirming PABP's presence in the BC1 RNP. Given the ubiquitous role of poly(A) regions in the retrotransposition process, these data suggest that PABP may contribute to the SINE retrotransposition process.

Base Sequence↗