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At least 1,135 records · Page 63Linked to original sources
PubMed2026

Global lessons from antibiotic resistance: Metformin-hydrolysing genes in transposable elements, a new threat for type II diabetic patients?

OBJECTIVES: To investigate the evolutionary origin, genomic mobility, and potential dissemination of metformin-hydrolysing genes (mfmAB), and to assess whether environmental selection by metformin pollution may drive the emergence of transferable pharmaceutical-degrading traits analogous to antibiotic resistance. METHODS: Large-scale comparative genomics was performed using publicly available bacterial genomes carrying mfmAB homologs. Phylogenomic reconstruction, average nucleotide identity analysis, genomic context comparison, plasmid characterization, and insertion sequence mapping were used to infer evolutionary history and identify mechanisms of horizontal gene transfer. RESULTS: mfmAB homologs were identified in twelve Aminobacter and three Pseudomonas genomes within a conserved ∼8.2 kb gene cluster. Phylogenomic analyses showed that metformin-degrading capacity emerged independently in multiple Aminobacter lineages across distinct continents, consistent with convergent evolution under anthropogenic selective pressure. Genomic comparisons indicated a chromosomal origin of mfmAB, followed by mobilization onto conjugative plasmids through IS1182-mediated transposition. In Pseudomonas, additional IS3/IS6-mediated transposition events integrated mfmAB into diverse plasmid backbones, frequently within composite transposons also encoding guanylurea and biguanide degradation pathways (guuH, bguH). These findings reveal a dynamic modular assembly of metabolic functions facilitating adaptation to pharmaceutical pollutants. CONCLUSIONS: Metformin pollution appears to promote the emergence and mobilization of pharmaceutical-degrading genes through mechanisms paralleling antibiotic resistance evolution. Although no clinical impact has yet been demonstrated, the potential spread of such genes into human-associated microbiomes and their possible co-selection with antibiotic resistance determinants represent an emerging One Health concern. Environmental surveillance of pharmaceutical-degrading genes is warranted to anticipate future threats to drug efficacy.

Convergent evolution↗
PubMed1997

Discovery of a Zdel transposable element in Zea species as a consequence of a retrotransposon insertion.

Nucleotide sequences similar to del1 retrotransposon from Lilium henryi have been discovered in Zea diploperennis as a consequence of finding a Zea retrotransposon element inserted into one of them. These sequences named Zdel (Zea del1-like) elements are present in all the Zea species (about 100 copies per haploid genome) and in Tripsacum dactyloides and absent from closely related genera. Sequences corresponding to gag and protease domains from a Zdel element have been identified. The Zdel protease sequence shows a conserved active site motif (DT/SG) from aspartic proteases. The high level of DNA methylation found in Zdel elements may be related to the observed absence of transcriptional activity.

Amino Acid Sequence↗
PubMed1997

Cloning and characterization of a copy of Tirant transposable element in Drosophila melanogaster.

A Tirant element, inserted at the 5' end of the mitochondrial glutamine synthetase (mt-gs) gene in a mutant allele giving rise to a recessive female sterility phenotype, was cloned and utilized to characterize this novel retrotransposable element of the Drosophila melanogaster genome. The 5.3 kb element present in the fs(2) PM11-19 mt-gs allele possesses a 417 bp long terminal repeat (LTR) at both ends. There is a serine tRNA binding site downstream of the 5' LTR sequence and a polypurine tract upstream of the 3' LTR end. The insertion leads to the duplication of a host-site CGCG sequence. In situ hybridization to salivary glands chromosomes showed evidence of the mobile nature of the element. The DNA sequencing of the cloned 5.3 kb element revealed that Tirant possesses an open reading frame (ORF) that shows similarity with the envelope protein encoded by the gypsy and 297 retrotransposons. In addition, the cloned element appears to be a subgenomic fragment of a not yet identified complete element, because only the integrase domain of the reverse transcriptase gene is found.

Amino Acid Sequence↗
PubMed2001

Double-stranded RNA-mediated silencing of genomic tandem repeats and transposable elements in the D. melanogaster germline.

BACKGROUND: The injection of double-stranded RNA (dsRNA) has been shown to induce a potent sequence-specific inhibition of gene function in diverse invertebrate and vertebrate species. The homology-dependent posttranscriptional gene silencing (PTGS) caused by the introduction of transgenes in plants may be mediated by dsRNA. The analysis of Caenorhabditis elegans mutants impaired with dsRNA-mediated silencing and studies in plants implicate a biological role of dsRNA-mediated silencing as a transposon-repression and antiviral mechanism. RESULTS: We investigated the silencing of testis-expressed Stellate genes by paralogous Su(Ste) tandem repeats, which are known to be involved in the maintenance of male fertility in Drosophila melanogaster. We found that both strands of repressor Su(Ste) repeats are transcribed, producing sense and antisense RNA. The Stellate silencing is associated with the presence of short Su(Ste) RNAs. Cotransfection experiments revealed that Su(Ste) dsRNA can target and eliminate Stellate transcripts in Drosophila cell culture. The short fragment of Stellate gene that is homologous to Su(Ste) was shown to be sufficient to confer Su(Ste)-dependent silencing of a reporter construct in testes. We demonstrated that Su(Ste) dsRNA-mediated silencing affects not only Stellate expression but also the level of sense Su(Ste) RNA providing a negative autogenous regulation of Su(Ste) expression. Mutation in the spindle-E gene relieving Stellate silencing also leads to a derepression of the other genomic tandem repeats and retrotransposons in the germline. CONCLUSIONS: Homology-dependent gene silencing was shown to be used to inhibit Stellate gene expression in the D. melanogaster germline, ensuring male fertility. dsRNA-mediated silencing may provide a basis for negative autogenous control of gene expression. The related surveillance system is implicated to control expression of retrotransposons in the germline.

Adenosine Triphosphatases↗
PubMed1997

Transposable elements: how non-LTR retrotransposons do it.

The source of the enzyme activity responsible for the transposition of retrotransposons of the type that lack terminal repeats has at last been identified: in L1Hs elements, it is encoded by the second open reading frame and is a nuclease related to the apurinic repair endonucleases.

Animals↗
PubMed1985

Structures of defective P transposable elements prevalent in natural Q and Q-derived M strains of Drosophila melanogaster.

Several DNA sequences with homology to the complete 2.9-kilobase (kb) P element from a P strain in the United States were isolated and characterized from two Drosophila melanogaster strains collected on Chichi Jima, an island 1000 km south of Tokyo. Except for a missing central region and trivial unsequenced regions of 38 base pairs, the 2.1-kb element isolated from a Q strain had the same DNA sequence as that of the complete P element. Seven other elements cloned from genomic DNAs of the Q strain and a Q-derived M strain all possessed the same restriction sites as those of the 2.9-kb P element except for one deleted region in each element. The finding of sequence conservation in P elements have had a common ancestor relatively recently. Thus, it is suggested that the P element family was a recent invader of the species. By contrast, no complete P element was found in these Japanese strains so far as surveyed, indicating the possibility that P elements in the Chichi Jima population are almost all defective. The implication of this possibility is discussed in relation to the uniqueness of the population on Chichi Jima where Q strains predominate and no P strains have yet been found.

Journal Article↗
PubMed1996

The hobo transposable element excises and has related elements in tephritid species.

Function of the Drosophila melanogaster hobo transposon in tephritid species was tested in transient embryonic excision assays. Wild-type and mutant strains of Anastrepha suspensa, Bactrocera dorsalis, B. cucurbitae, Ceratitis capitata, and Toxotrypana curvicauda all supported hobo excision or deletion both in the presence and absence of co-injected hobo transposase, indicating a permissive state for hobo mobility and the existence of endogenous systems capable of mobilizing hobo. In several strains hobo helper reduced excision. Excision depended on hobo sequences in the indicator plasmid, though almost all excisions were imprecise and the mobilizing systems appear mechanistically different from hobo. hobo-related sequences were identified in all species except T. curvicauda. Parsimony analysis yielded a subgroup including the B. cucurbitae and C. capitata sequences along with hobo and Hermes, and a separate, more divergent subgroup including the A. suspensa and B. dorsalis sequences. All of the sequences exist as multiple genomic elements, and a deleted form of the B. cucurbitae element exists in B. dorsalis. The hobo-related sequences are probably members of the hAT transposon family with some evolving from distant ancestor elements, while others may have originated from more recent horizontal transfers.

Amino Acid Sequence↗
PubMed1981

The 5' termini of RNAs encoded by the transposable element copia.

The 5' termini of copia-specific RNAs in Drosophila melanogaster tissue culture cells were determined by S1 nuclease mapping and cap analysis. Both major copia RNAs share an identical set of heterogeneous 5' ends. Three major cap 1 structures M7GpppCmpUp, M7GpppCmpCp and M7GpppGmpUp together with several other minor caps were found. Almost all the 5' termini, as judged by S-1 nuclease mapping, were located either in a pyrimidine-rich part of the terminal direct repeat or apparently outside of the copia element, suggesting that a proportion of copia transcripts derive from promoters external to the genetic element.

Animals↗
PubMed2001

Engineering variegated floral patterns in tobacco plants using the Arabidopsis transposable element Tag1.

Variegated flower phenotypes were generated using the Arabidopsis transposon Tag1 and the maize R regulatory gene. Tag1 was inserted between the CaMV 35S promoter and the maize R gene and transformed into tobacco plants. In half of the transgenic plants, variegated flower patterns were observed. Each line had a different pattern, with varying intensities with three lines showing only tiny sectors indicative of late excision and one showing large sectors indicative of earlier excision.

Arabidopsis↗
PubMed1999

Genomic demography: a life-history analysis of transposable element evolution.

Retrotransposons are ubiquitous mobile genetic elements that have played a significant role in shaping eukaryotic genome evolution. The genome of the yeast Saccharomyces cerevisiae harbours five families of retrotransposons, Ty1-Ty5. With the publication of the S. cerevisiae genome sequence, for the first time a full genomic complement of retrotransposon sequences is available. Analysis of these sequences promises to yield insight into the nature of host--transposon coevolution. Evolutionary change in Ty elements depends on their replication and excision rates, which have been determined in the laboratory. Rates measured in the laboratory may differ from those that have operated over evolutionary time. Based on an analysis of sequence data for the Ty1, Ty2 and hybrid Ty1/2 families, we develop a novel 'genomic demography' model to estimate long-term transposition and excision rates and to estimate how long ago these elements entered the yeast genome. We find that rates of excision and transposition have averaged 7.2-8.7 x 10(-8) per generation over evolutionary time. Two separate models provide upper- and lower-bound estimates for the age of the system, suggesting that the first elements entered the genome between approximately 50 million and 250 million generations ago.

Evolution, Molecular↗
PubMed1998

Transposable elements and genome organization: a comprehensive survey of retrotransposons revealed by the complete Saccharomyces cerevisiae genome sequence.

We conducted a genome-wide survey of Saccharomyces cerevisiae retrotransposons and identified a total of 331 insertions, including 217 Ty1, 34 Ty2, 41 Ty3, 32 Ty4, and 7 Ty5 elements. Eighty-five percent of insertions were solo long terminal repeats (LTRs) or LTR fragments. Overall, retrotransposon sequences constitute >377 kb or 3.1% of the genome. Independent evolution of retrotransposon sequences was evidenced by the identification of a single-base pair insertion/deletion that distinguishes the highly similar Ty1 and Ty2 LTRs and the identification of a distinct Ty1 subfamily (Ty1'). Whereas Ty1, Ty2, and Ty5 LTRs displayed a broad range of sequence diversity (typically ranging from 70%-99% identity), Ty3 and Ty4 LTRs were highly similar within each element family (most sharing >96% nucleotide identity). Therefore, Ty3 and Ty4 may be more recent additions to the S. cerevisiae genome and perhaps entered through horizontal transfer or past polyploidization events. Distribution of Ty elements is distinctly nonrandom: 90% of Ty1, 82% of Ty2, 95% of Ty3, and 88% of Ty4 insertions were found within 750 bases of tRNA genes or other genes transcribed by RNA polymerase III. tRNA genes are the principle determinant of retrotransposon distribution, and there is, on average, 1.2 insertions per tRNA gene. Evidence for recombination was found near many Ty elements, particularly those not associated with tRNA gene targets. For these insertions, 5'- and 3'-flanking sequences were often duplicated and rearranged among multiple chromosomes, indicating that recombination between retrotransposons can influence genome organization. S. cerevisiae offers the first opportunity to view organizational and evolutionary trends among retrotransposons at the genome level, and we hope our compiled data will serve as a starting point for further investigation and for comparison to other, more complex genomes.

Base Sequence↗
PubMed1996

Molecular structure of the transposable element ninja in Drosophila simulans.

Genetically unstable DNA sequences of 16.1 kb in length were isolated from the white locus of the W(mky) strain of Drosophila simulans. This insertional DNA has some unique characteristics as a transposon. It is found in high numbers in this strain and its revertant strains W(psm1) and W(cho), but not elsewhere, and the sequence is a tandem triplication of a basic repeating unit. In order to determine the structure of the insert as whole and the functional unit as a transposon, we analyzed nine clones isolated from genomic libraries of W(psm1) and W(cho). The repeating unit of the 16.1 kb insertion was the retrotransposon ninja and the DNA sequence of the entire element was determined. The ninja transposon is 6644 bp in length, with a 316 bp long terminal repeat (LTR) on each end. It contains two openreading frames (ORFs), and the pol region is divided between the two ORFs in contrast the organization of other retrotransposons. An alignment analysis of the reverse transcriptase sequences suggested that the ninja element is the first Drosophila retrotransposon belonging to the Pao subgroup.

Amino Acid Sequence↗