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PubMed2004

[How bacteria resist antibiotics: a primary form of collective intelligence?].

Bacteria produce inhibitory enzymes (beta-lactamases, etc), block antibiotic attachment to target molecules (MRSA, etc.), extrude antibiotics from the cell by active efflux systems (multidrug resistant pseudomonas, etc) or limit antibiotic penetration through the outer membrane in Gram negatives. Genetically, resistance occurs after mutation or horizontal transfers (transformation, transduction, conjugation) of mobile genetic elements (integrons, transposons, phages, plasmids), associated with a risk of epidemic spread. Recent data stress the importance pheromones for facilitating inter-bacterial genetic exchanges. Activated by quinolones and penicillins the SOS response augments the mutation rate (by about 10,000 fold) and liberates mobile genetic elements offering more opportunities to select resistance. These highly pertinent non-darwinian systems raise the hypothesis of a primary form of intelligence developed already 3.8 billions years ago.

Anti-Bacterial Agents↗
PubMed2004

Evolution of Staphylococcus aureus by large chromosomal replacements.

Conjugative transfer and replacement of hundreds of kilobases of a bacterial chromosome can occur in vitro, but replacements in nature are either an order of magnitude smaller or involve the movement of mobile genetic elements. We discovered that two lineages of Staphylococcus aureus, including a pandemic methicillin-resistant lineage, were founded by single chromosomal replacements of at least approximately 244 and approximately 557 kb representing approximately 10 and approximately 20% of the chromosome, respectively, without the obvious involvement of mobile genetic elements. The replacements are unprecedented in natural populations of bacteria because of their large size and unique structure and may have a dramatic impact on bacterial evolution.

Base Sequence↗
PubMed2003

Structural and functional characteristics of homing endonucleases.

Mobile genetic elements constitute a remarkably diverse group of nonessential selfish genes that provide no apparent function to the host. These selfish genes have been implicated in host extinction, speciation and architecture of genetic systems. Homing endonucleases, encoded by the open reading frames embedded in introns or inteins of mobile genetic elements, possess double-stranded DNA-specific endonuclease activity. They inflict sequence-specific double-strand breaks at or near the homing site in intron- or intein-less allele. Subsequently, through nonreciprocal exchange the insertion sequence (intron or intein) is transferred from an intein- or intron-containing allele to an intein- or intron-less allele. The components of host double-strand break repair pathway are thought to finish the "homing" process. Several lines of evidence suggest that homing endonucleases are capable of promoting transposition into ectopic sites within or across genomes for their survival as well as dispersal in natural populations. The occurrence of inteins at high frequencies serves as instructive models for understanding the mechanistic aspects of the process of homing and its evolution. This review focuses on genetic, biochemical, structural, and phylogenetic aspects of homing endonucleases, and their comparison with restriction endonucleases.

Amino Acid Motifs↗
PubMed2026

Optimizing a culture-enriched hybrid metagenomics pipeline to assess the AMR footprint of livestock manure in anaerobic digestate.

The role of environmental samples from livestock production systems, including manure and anaerobic digestate, as reservoirs of antimicrobial resistance genes (ARGs) is likely underestimated because conventional metagenomic approaches can overlook low-abundance ARGs and often lack the resolution to associate these genes with their microbial hosts and co-localized mobile genetic elements (MGEs). We evaluated whether culture-enriched metagenomics (CEMG), with and without antibiotic selection, enhances ARG detection in anaerobic digestate and improves the resolution of ARG-MGE-host associations using hybrid short- and long-read metagenomic assembly. CEMG increased ARG recovery; mean ARG abundance rose from 15.4 counts per million (CPM) in metagenomic fresh digestate (FD) to 124 CPM in CEMG without antibiotics and 160 CPM in antibiotic-selective CEMG. In FD, only 9 unique ARGs were detected, whereas CEMG recovered 112, including ARGs of clinical importance, such as glycopeptide resistance, beta-lactamase genes, and the cfr 23S rRNA methyltransferase conferring cross-resistance to multiple antibiotic classes. Antibiotic selection induced targeted, class-specific shifts in ARG profiles, with ARGs associated with tetracycline resistance consistently enriched across treatments. Hybrid metagenomic assembly resolved the genomic context of 784 ARGs, of which 59.3% were co-localized with at least one class of MGEs, predominantly plasmids and integrative conjugative elements/integrative mobilizable elements. Biocide and metal resistance genes frequently co-occurred with ARGs on the same contigs. Together, these findings demonstrate that antibiotic-selective culture enrichment enhances resistome surveillance by improving detection of low-abundance ARGs, while hybrid assembly provides critical genomic context for assessing their mobility and host associations.IMPORTANCELivestock manure and its byproducts, such as anaerobic digestate, are recognized as important environmental reservoirs of antimicrobial resistance genes (ARGs) and resistant bacteria, yet current metagenomic approaches may underestimate this risk by failing to detect low-abundance but clinically relevant ARGs. Here, we show that integrating culture enrichment with hybrid metagenomics improves ARG recovery and reveals ARG co-localization with mobile genetic elements and putative bacterial hosts. This approach captures a cultivable and condition-responsive fraction of the resistome that is not readily accessible through direct metagenomic sequencing alone, providing a more informative framework for environmental AMR surveillance.

anaerobic digestion↗
PubMed1993

Integrons: novel DNA elements which capture genes by site-specific recombination.

Integrons are unusual DNA elements which include a gene encoding a site-specific DNA recombinase, a DNA integrase, and an adjacent site at which a wide variety of antibiotic resistance and other genes are found as inserts. One or more genes can be found in the insert region, but each gene is part of an independent gene cassette. The inserted genes are expressed from a promoter in the conserved sequences located 5' to the genes, and integrons are thus natural expression vectors. A model for gene insertion in which circular gene cassettes are inserted individually via a single site-specific recombination event has been proposed and verified experimentally. The gene cassettes include a gene coding region and, at the 3' end of the gene an imperfect inverted repeat, a 59-base element. The 59-base elements are a diverse family of elements which function as sites recognized by the DNA integrase. Site-specific insertion of individual genes thus represents a further mechanism which contributes to the evolution of the genomes of Gram-negative bacteria and their plasmids and transposons. Members of the most studied class of integrons, which include the sulI gene in the conserved sequences, are believed to be mobile DNA elements on the basis that they are found in many independent locations, and a discrete boundary is found at the outer end of the 5'-conserved segment. However, the length of the 3'-conserved segment is variable in the integrons examined to date, and it is likely that this variability has arisen as the result of insertion and deletion events. Though the true extent of the 3'-conserved segment remains to be determined, it seems likely that these integrons are mobile DNA elements. The second known class of integrons comprises members of the Tn7 transposon family.

Base Sequence↗
PubMed1996

Vector for IS element entrapment and functional characterization based on turning on expression of distal promoterless genes.

We constructed and characterized a novel trap vector for rapid isolation of insertion sequences. The strategy used for the isolation of IS elements is based on the ability of many IS elements to turn on the expression of otherwise silent genes distal to some sites of insertion. The simple transposition of an IS element can sometimes cause the constitutive expression of promoterless antibiotic resistance genes resulting in selectable phenotypes. The trap vector pAW1326 is based on a pBR322 replicon, it carries ampicillin and streptomycin resistance genes, and also silenced genes that confer chloramphenicol and kanamycin resistance once activated. The trap vector pAW1326 proved to be efficient and 85 percent of all isolated mutations were insertions. The majority of IS elements resident in the studied Escherichia coli strains tested became trapped, namely IS2, IS3, IS5, IS150, IS186 and Tn1000. We also encountered an insertion sequence, called IS10L/R-2, which is a hybrid of the two IS variants IS10L and IS10R. IS10L/R-2 is absent from most E. coli strains, but it is detectable in some strains such as JM109 which had been submitted to Tn10 mutagenesis. The distribution of the insertion sequences within the trap region was not random. Rather, the integration of chromosomal mobile genetic elements into the offered target sequence occurred in element-specific clusters. This is explained both by the target specificity and by the specific requirements for the activation of gene transcription by the DNA rearrangement. The employed trap vector pAW1326 proved to be useful for the isolation of mobile genetic elements, for a demonstration of their transposition activity as well as for the further characterization of some of the functional parameters of transposition.

DNA Transposable Elements↗
PubMed1985

The Vi element. A transposon-like repeated DNA sequence interspersed in the vitellogenin locus of Xenopus laevis.

A repeated DNA element in Xenopus laevis is described that is present in about 7500 copies dispersed throughout the genome. It was first identified in the 5' flanking region of one vitellogenin gene and was therefore named the Vi element. Seven copies are present within the vitellogenin gene region, three of them within introns of the genes A1, A2 and B2, and the other four copies in the gene flanking regions. Four of these copies have been sequenced. The Vi element is bounded by a well-conserved 13 base-pair inverted repeat; in addition, it is flanked by a three base-pair direct repeat that appears to be site-specific. The length of these four copies varies from 112 to 469 base-pairs; however, sequence homology between the different copies is very high. Their structural characteristics suggest that length heterogeneity may have arisen by either unequal recombinations, deletions or tandem duplications. Altogether, the characteristics and properties of the Vi element indicate that it might represent a mobile genetic element. One of the four copies sequenced is inserted close (position -535) to the transcription initiation site of the vitellogenin gene B2 in a region otherwise showing considerable homology with the closely related gene B1. Nevertheless, the presence of the Vi element does not seem to influence significantly the estrogen-controlled expression of gene B2. In addition, three alleles of this gene created by length polymorphism in intron 3 and in the Vi element inserted near the transcription initiation site are described.

Animals↗
PubMed2004

Isolation and characterization of active LINE and SINEs from the eel.

Long interspersed elements (LINEs) and short interspersed elements (SINEs) are retrotransposons. These elements can mobilize by the "copy-and-paste" mechanism, in which their own RNA is reverse-transcribed into complementary DNA (cDNA). LINEs and SINEs not only are components of eukaryotic genomes but also drivers of genomic evolution. Thus, studies of the amplification mechanism of LINEs and SINEs are important for understanding eukaryotic genome evolution. Here we report the characterization of one LINE family (UnaL2) and two SINE families (UnaSINE1 and UnaSINE2) from the eel (Anguilla japonica) genome. UnaL2 is approximately 3.6 kilobases (kb) and encodes only one open reading frame (ORF). UnaL2 belongs to the stringent type--thought to be a major group of LINEs--and can mobilize in HeLa cells. We also show that UnaL2 and the two UnaSINEs have similar 3' tails, and that both UnaSINE1 and UnaSINE2 can be mobilized by UnaL2 in HeLa cells. These elements are thus useful for delineating the amplification mechanism of stringent type LINEs as well as that of SINEs.

Amino Acid Sequence↗
PubMed1994

Identification of positive and negative transcriptional regulatory elements of the rabbit angiotensin-converting enzyme gene.

The two tissue-specific mRNAs encoding the isozymes of rabbit angiotensin-converting enzyme (ACE) are generated from the same gene by alternative choice of two transcription initiation sites 5.7 kb apart. In the current study, we have characterized the regulatory sites controlling the transcription of the larger pulmonary isozyme mRNA. For this purpose, reporter genes driven by varying lengths of upstream region of the ACE gene were transfected into ACE-producing cells. Our results demonstrated that the transcription of this gene is primarily driven by positive elements within the first 274 bp DNA upstream of the transcription initiation site. The reporter gene driven by this region was expressed in two ACE-producing cells but not in two ACE-non-producing cells thereby establishing its tissue specificity. Our experiments also revealed the existence of a strong negative element located between -692 and -610 positions. This element suppressed the expression of the reporter gene in a dose-dependent and position and orientation-independent fashion thus suggesting that it is a true silencer element. It could also repress the expression of a reporter gene driven by the heterologous strong promoter of the beta-actin gene. The repressing effects of the negative element could be partially overcome by cotransfecting the isolated negative element along with the reporter gene containing the negative element. This result was possibly due to the functional removal of a limiting trans-acting factor which binds to this element. Electrophoretic mobility shift assays revealed that the negative element can form several complexes with proteins present in the nuclear extract of an ACE-producing cell line. At least part of the negative element is strongly conserved in the upstream regions of the human and mouse ACE genes.

Animals↗
PubMed2003

Mobile genes coding for efflux-mediated antimicrobial resistance in Gram-positive and Gram-negative bacteria.

Efflux mechanisms that account for resistance to a variety of antimicrobial agents are commonly found in a wide range of bacteria. Two major groups of efflux systems are known, specific exporters and transporters conferring multidrug resistance (MDR). The MDR systems are able to remove antimicrobials of different classes from the bacterial cell and occasionally play a role in the intrinsic resistance of some bacteria to certain antimicrobials. Their genes are commonly located on the bacterial chromosome. In contrast, the genes coding for specific efflux systems are often associated with mobile genetic elements which can easily be interchanged between bacteria. Specific efflux systems have mainly been identified with resistances to macrolides, lincosamides and/or streptogramins, tetracyclines, as well as chloramphenicol/florfenicol in Gram-positive and Gram-negative bacteria. In this review, we focus on the molecular biology of antimicrobial resistance mediated by specific efflux systems and highlight the association of the respective resistance genes with mobile genetic elements and their distribution across species and genus borders.

Anti-Bacterial Agents↗
PubMed2026

PCR analysis of insertion sequences leads to the generation of artefact amplicons.

Insertion sequences (ISs) are small, self-mobilizing DNA elements widespread across prokaryotic genomes, including chromosomes and plasmids. IS elements frequently co-localize with antimicrobial resistance (AMR) genes and mediate their mobilization, often as part of larger genomic structures that encompass multiple IS elements and antibiotic resistance genes. In this study, we employed Polymerase Chain Reaction (PCR) to amplify DNA sequences containing two copies of an IS26 element from two Escherichia coli ST131 isolates. While the respective PCRs generated products of the expected size, we also observed multiple amplicons of unexpected sizes, which could be misinterpreted as population heterogeneity attributed to IS mobilization. By extracting, re-amplifying and sequencing individual PCR products, we demonstrate that these amplicons of unexpected sizes were indeed artefact products generated during the PCR reaction, likely mediated by within-PCR recombination of the IS26 sequences. Furthermore, PCRs with equally oriented primers, each located close to an IS26 element, also generated artefact amplicons. This research highlights the limitations of using PCR to assess DNA sequences encoding multiple copies of an IS element and therefore, the presence of these genomic structures or the mobilization of the respective IS elements should not be assessed by diagnostic PCR alone but be corroborated with complementary techniques.

ESBL↗
PubMed2026

Widespread horizontal transfer and strong selection enhance microbial adaptation in Antarctic soils.

Terrestrial Antarctica harbors compositionally diverse and functionally distinct microbial life. Yet the eco-evolutionary processes underlying adaptation to Antarctica's polyextreme conditions remain largely unknown. Here, we address how horizontal gene transfer (HGT) and de novo mutations influence microbial adaptation in 16 Antarctic soils using combined short- and long-read datasets. Phylogenetic reconciliation and mobile genetic element analysis of 676 metagenome-assembled genomes show frequent HGT across communities. While transferred genes span diverse functional categories, those involved in energy metabolism are exchanged at higher frequency. Genes for aerotrophy, i.e. the consumption of atmospheric trace gases to provide energy, carbon, and hydration, are among the most frequently disseminated. Approximately a quarter of carbon monoxide dehydrogenases and [NiFe]-hydrogenases are predicted to be horizontally acquired and are often associated with mobile genetic elements. Analysis of polymorphisms suggests widespread purifying selection, particularly for aerotrophy genes, providing further evidence that aerotrophy is critical for microbial survival in Antarctica. Genetic variation in hydrogenases is tightly associated with predicted protein structures, with intense selection acting on critical sites preserving stability and function. Together, these findings show that previously unrecognized eco-evolutionary dynamics shape the composition and function of Antarctic microbial communities, and confirm aerotrophy is a strongly selected and horizontally disseminated trait.

Antarctic Regions↗
PubMed2005

[Genomic variability of vibrio cholerae El Tor biovariant strains].

The authors performed comparative analysis of the genomes of 145 clinical and environmental isolates of Vibrio cholerae El Tor biovariants using single locus and multiplex PCR. The study found that clinical strains isolated from patients with cholera formed a genetically homogenous group, where bacterial chromosome contained all the tested virulence genes, situated on mobile genetic elements that had been acquired by the pathogen at various stages of its evolution. Strains isolated from water ecosystems during interepidemic period were heterogeneous and formed three groups: a small number of virulent strains; non-toxigenic vibrio strains that, in the process of reductional variation in their new econiche, had only managed to maintain individual virulence genes; non-pathogenic "water" vibrios, whose chromosome contained only the genes from its core part, mobile genetic elements being optionally represented only by the persistence island. Molecular typing established genetic relations among V. cholerae strains under study.

Chromosomes, Bacterial↗
PubMed2005

Distributions of arsenic and essential elements in pinna of arsenic hyperaccumulator Pteris vittata L.

The distributions of arsenic and 6 essential elements in the pinna of As hyperaccumulator, Pteris vittata L., were studied using synchrotron radiation X-ray fluorescence (SRXRF). Significant correlation between the distribution and mobility of the elements revealed that SRXRF study on the elemental distribution was feasible to inspect the transportations of elements in plants. The distribution of As in the pinna showed that As had great abilities to be transported in xylem vessels and from xylem to mesophyll. The distribution of K, one of the most mobile elements in plants, was similar to that of As, whereas the distributions of Fe and Ca with less mobility in plants were almost opposite to that of As in the pinna.

Arsenic↗
PubMedDate not supplied

[Genetic effects in Drosophila melanogaster induced by chronic low-dose irradiation].

It was investigated the influence of the chronic gamma-irradiation in the dose rate of 0.17 sGy/h on the rate of genetic variability in the laboratory strains of Drosophila melanogaster with genotypic distinguishes in mobile genetic elements and defects in the DNA repair processes. It was shown that the rates of induction of recessive lethal mutations depended on genotype of investigated strains. In the different strains we have observed an increase as well as a decrease of the mutation rate. Also in was established that irradiation leads to the frequencies of the GD-sterility and mutability of the snw and h(w+) in the P-M and H-E dysgenic crosses. The obtained results suggest that mobile genetic elements play an important role in the forming of genetic effects in response to low dose irradiation.

Animals↗
PubMed2002

Bacterial group II introns in a deep-sea hydrothermal vent environment.

Group II introns are catalytic RNAs and mobile retrotransposable elements known to be present in the genomes of some nonmarine bacteria and eukaryotic organelles. Here we report the discovery of group II introns in a bacterial mat sample collected from a deep-sea hydrothermal vent near 9 degrees N on the East Pacific Rise. One of the introns was shown to self-splice in vitro. This is the first example of marine bacterial introns from molecular population structure studies of microorganisms that live in the proximity of hydrothermal vents. These types of mobile genetic elements may prove useful in improving our understanding of bacterial genome evolution and may serve as valuable markers in comparative studies of bacterial communities.

Amino Acid Sequence↗
PubMed2000

[The level of dysgenic sterility and recessive mutations induced in laboratory strains of Drosophila melanogaster exposed to chronic low-dose gamma irradiation].

Recent investigations showed that genetic instability accounts for many radiobiological effects. However, mechanisms underlying this phenomenon are still poorly understood. Assuming that mobile genetic elements may be involved in the induction of genetic instability, we studied parameters that characterize the activity of these elements in Drosophila melanogaster: hybrid dysgenesis and the level of recessive lethal mutations. In our experiments, we used D. melanogaster strains that differed in the type of hybrid dysgenesis (P-M and H-E). It was demonstrated that chronic exposure to radiation leads to substantial changes in the genetic structure of a population and an enhanced level of dysgenic sterility. Our results indicate that genetic instability and adaptation to the effect of chronic gamma-radiation are associated with the radiation-induced mobilization of mobile genetic elements.

Animals↗