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PubMed2006

Complete genome sequence of USA300, an epidemic clone of community-acquired meticillin-resistant Staphylococcus aureus.

BACKGROUND: USA300, a clone of meticillin-resistant Staphylococcus aureus, is a major source of community-acquired infections in the USA, Canada, and Europe. Our aim was to sequence its genome and compare it with those of other strains of S aureus to try to identify genes responsible for its distinctive epidemiological and virulence properties. METHODS: We ascertained the genome sequence of FPR3757, a multidrug resistant USA300 strain, by random shotgun sequencing, then compared it with the sequences of ten other staphylococcal strains. FINDINGS: Compared with closely related S aureus, we noted that almost all of the unique genes in USA300 clustered in novel allotypes of mobile genetic elements. Some of the unique genes are involved in pathogenesis, including Panton-Valentine leucocidin and molecular variants of enterotoxin Q and K. The most striking feature of the USA300 genome is the horizontal acquisition of a novel mobile genetic element that encodes an arginine deiminase pathway and an oligopeptide permease system that could contribute to growth and survival of USA300. We did not detect this element, termed arginine catabolic mobile element (ACME), in other S aureus strains. We noted a high prevalence of ACME in S epidermidis, suggesting not only that ACME transfers into USA300 from S epidermidis, but also that this element confers a selective advantage to this ubiquitous commensal of the human skin. INTERPRETATION: USA300 has acquired mobile genetic elements that encode resistance and virulence determinants that could enhance fitness and pathogenicity.

Community-Acquired Infections↗
PubMed2006

The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome.

We determined the complete genome sequence of Clostridium difficile strain 630, a virulent and multidrug-resistant strain. Our analysis indicates that a large proportion (11%) of the genome consists of mobile genetic elements, mainly in the form of conjugative transposons. These mobile elements are putatively responsible for the acquisition by C. difficile of an extensive array of genes involved in antimicrobial resistance, virulence, host interaction and the production of surface structures. The metabolic capabilities encoded in the genome show multiple adaptations for survival and growth within the gut environment. The extreme genome variability was confirmed by whole-genome microarray analysis; it may reflect the organism's niche in the gut and should provide information on the evolution of virulence in this organism.

Adaptation, Physiological↗
PubMed2004

Ty1 mobilizes subtelomeric Y' elements in telomerase-negative Saccharomyces cerevisiae survivors.

When telomerase is inactivated in Saccharomyces cerevisiae, telomeric DNA shortens with every cell division, and cells stop dividing after approximately 100 generations. Survivors that form in these senescent populations and resume growing have variably amplified arrays of subtelomeric Y' elements. We marked a chromosomal Y' element with the his3AI retrotransposition indicator gene and found that Y'HIS3 cDNA was incorporated into the genome at approximately 10- to 1,000-fold-higher frequencies in survivors compared to telomerase-positive strains. Y'HIS3 cDNA mobility was significantly reduced if assayed at 30 degrees C, a nonpermissive temperature for Ty1 retrotransposition, or in the absence of Tec1p, a transcription factor for Ty1. Microarray analysis revealed that Y' RNA is preferentially associated with Ty1 virus-like particles (VLPs). Genomic copies of Y'HIS3 cDNA typically have downstream oligo(A) tracts, followed by a complete Ty1 long terminal repeat and TYA1 or TYB1 sequences. These data are consistent with the use of Ty1 cDNA to prime reverse transcription of polyadenylated Y' RNA within Ty1 VLPs. Unmarked Y'-oligo(A)-Ty1 cDNA was also detected in survivors, reaching copy numbers of approximately 10(-2) per genome. We propose that Y'-oligo(A)-Ty1 cDNA recombines with Y' elements at eroding telomeres in survivors and may play a role in telomere maintenance in the absence of telomerase.

Base Sequence↗
PubMed1999

The role of interelement selection in Saccharomyces cerevisiae Ty element evolution.

Retrotransposons are mobile genetic elements that are ubiquitous components of eukaryotic genomes. The evolutionary success of retrotransposons is explained by their ability to replicate faster than the host genomes in which they reside. Elements with higher rates of genomic replication possess a selective advantage over less active elements. Retrotransposon populations, therefore, are shaped largely by selective forces acting at the genomic level between elements. To evaluate rigorously the effects of selective forces acting on retrotransposons, detailed information on the patterns of molecular variation within and between retrotransposon families is needed. The sequencing of the Saccharomyces cerevisiae genome, which includes the entire genomic complement of yeast retrotransposons, provides an unprecedented opportunity to access and analyze such data. In this study, we analyzed in detail the patterns of nucleotide variation within the open reading frames of two parental (Ty1 and Ty2) and one hybrid (Ty1/2) family of yeast retrotransposons. The pattern and distribution of nucleotide changes on the phylogenetic reconstructions of the three families of Ty elements reveal evidence of negative selection on both internal and external branches of the Ty phylogenies. These results indicate that most, if not all, Ty elements examined represent active or recently active retrotransposon lineages. We discuss the relevance of these findings with respect to the coevolutionary dynamic operating between genomic element populations and the host organisms in which they reside.

Databases, Factual↗
PubMed2025

Transition of Staphylococcus aureus tetracycline resistance plasmid pT181 from independent multicopy replicon to predominantly integrated chromosomal element over 65 years.

Mobile genetic elements (MGEs), including plasmids, phages and genome islands, are major sources of bacterial genetic diversity. The small plasmid pT181 confers tetracycline resistance in bacterial pathogen Staphylococcus aureus via an efflux pump, TetK. pT181 was one of the earliest sequenced S. aureus plasmids, and has been isolated in both clinical and livestock-associated strains for decades, both as an independent replicon and integrated in the chromosome as part of staphylococcal cassette chromosome mec (SCCmec). Bacterial genome analysis tools and high-quality sequences with metadata are publicly available, but these resources remain underleveraged for examining historical data, especially when studying the spread of MGEs across a species and over time. Using publicly available reads and metadata, we explored the evolution of pT181 over almost seven decades of samples to identify temporal trends in sequence evolution, copy number changes, and spread across S. aureus and beyond. pT181 was prevalent across S. aureus (found in 9.5% of 83,366 genomes tested), with a conserved sequence outside of three hypervariable regions. The history of pT181 since 1954 is characterized by spread across strains, significant variation in plasmid copy number of the independent replicon, and increasing frequency of integration of the plasmid into the S. aureus chromosome. We have identified multiple chromosomal integration locations of the plasmid, including outside of the previously characterized SCCmec. We find that pT181 has been transferred across staphylococcaceae and into a Gram-negative species. The repeated integration of pT181 into the chromosome may indicate co-evolution of the plasmid and the host, potentially to facilitate increased antibiotic resistance.

Journal Article↗
PubMed1998

Multiplex polymerase chain reaction of Alu polymorphic insertions.

Alu sequences are present in humans in excess of 500,000 copies per haploid genome and represent the largest family of short interspersed repetitive elements (SINEs). These mobile genetic elements are ancestrally derived from the 7SL RNA gene and move throughout the genomes of primates by retroposition. Polymorphic Alu insertions have proven to be useful for population studies, paternity determinations and forensic applications. Additionally, a simple polymerase chain reaction (PCR)-based assay has been established to examine these polymorphisms. In the present study, we have applied the technique of multiplex polymerase chain reaction to the Alu polymorphic system. Duplex and triplex PCR reactions were performed for the analysis of five different Alu polymorphic loci in different combinations. This study represents a starting point for further experimentation to improve and eventually optimize Alu multiplex PCR.

Alu Elements↗
PubMed1985

Interaction between mobile DNA-element-induced lethal mutations and chemical mutagens in the hybrid dysgenic system of Drosophila melanogaster.

Using the sex-linked recessive lethal mutation screen, a synergistic interaction is observed for mutations induced by chemical mutagens (ethyl methanesulfonate and dimethylnitrosamine) and the transposable DNA-element system of hybrid dysgenesis in spermatogonial cells of Drosophila melanogaster. Although the mechanism of this interaction is unknown, these results suggest that some chemical mutagens may induce transpositions, hybrid dysgenic cells may be more sensitive to chemically induced genetic damage, or hybrid dysgenesis may inhibit the efficiency of repair of chemically induced lesions.

Animals↗
PubMed1987

Mobilization of hobo elements residing within the decapentaplegic gene complex: suggestion of a new hybrid dysgenesis system in Drosophila melanogaster.

We present results demonstrating that the hobo family of transposable elements can promote high rates of chromosomal instability. Using strains with a hobo element inserted within the decapentaplegic gene complex (DPP-C), we have recovered numerous DPP-C mutations involving chromosomal rearrangements and deletions with one endpoint in the vicinity of the pre-existing hobo element. This hypermutability occurred in the germ lines of hybrid progeny from crosses involving strains containing hobo elements to strains lacking them. In some crosses, the offspring had rudimentary gonads, reminiscent of GD sterility. The germline hypermutability and infertility are similar to those produced by P-element-mediated hybrid dysgenesis. Given the many genetic and molecular similarities of the P and hobo systems, we propose that a system analogous to P-M hybrid dysgenesis has been activated in the hobo+ X hobo- crosses.

Alleles↗
PubMed1995

Identification of sequences which regulate the expression of Drosophila melanogaster Doc elements.

Long interspersed nuclear elements (LINEs) are mobile DNA elements which propagate by reverse transcription of RNA intermediates. LINEs lack long terminal repeats, and their expression is controlled by promoters located inside to the transcribed region of unit-length DNA copies. Doc elements constitute one of the seven families of LINEs found in Drosophila melanogaster. Plasmids in which the chloramphenicol acetyltransferase (CAT) gene is preceded by DNA segments from different Doc family members were used as templates for transient expression assays in Drosophila S2 cells. Transcription is initiated at the 5' end of Doc elements within hexamers fitting the consensus (C/G)AYTCG and is regulated by a DNA region which is located approximately 20 base pairs (bp) downstream from the RNA start site(s). The region includes a sequence (RGACGTGY motif, or DE2) which stimulates transcription in other Drosophila LINEs, and two adjacent elements, DE1 and DE3. Moving the downstream region either 4 bp away from, or 5 bp closer to the RNA start site region inhibited transcription. Sequences located approximately 200 bp downstream from the Doc 5' end repressed CAT expression in an orientation- and position-dependent manner. The inhibition reflects impaired translation of the CAT gene possibly consequent to the interaction of specific Doc RNA sequences with a cellular component.

Animals↗
PubMed1981

Mobile dispersed genetic element MDG1 of Drosophila melanogaster: nucleotide sequence of long terminal repeats.

Long terminal repeats (LTRs) of two members of mdg1 family were sequenced. In the both cases, they are represented by perfect direct repeats 442 and 444 bp in length. Sixteen nucleotides in the LTRs of two different mdg1 elements are different. Each LTR contains slightly mismatched 16-nucleotide inverted repeats located at the ends of the LTR. Six base pairs closest to the termini of LTR form perfect inverted repeats. On the gene-distal sides of LTRs, short 4-nucleotide direct repeats are located, probably representing the duplication of a target DNA sequence arising from insertion of mdg. They are different in the two cases analyzed. Just as the other analyzed eukaryotic transposable elements, mdg1 starts with TGT and ends with ACA. Within the both strands of LTR, the sequences similar to Hogness box (a putative signal for RNA initiation, or a selector) and AATAAA blocks (putative polyadenylation signals) are present. The LTR of mdg1 contains many short direct and inverted repetitive sequences. These include a 10-nucleotide sequence forming a perfect direct repeat with the first ten nucleotides of the LTR. A region of LTR about 70 bp long is represented by simple repetitive sequences (TAT).

Animals↗
PubMed1990

Laterally mobile, cortical tension elements can self-assemble into a contractile ring.

Animal cells cleave by the progressive constriction of an equatorial region. The plane of the constricting equator is orthogonal to the mitotic spindle axis and is positioned so that the spindle is bisected, thus ensuring equipartitioning of the chromosomes. Constriction is achieved by the active contraction of a circumferential band of actomyosin-containing filaments. The mitotic apparatus is necessary for the formation of the contractile ring and specifies its position and orientation; however, it takes no active part in furrowing. One of the central questions that has to be answered to understand cytokinesis is: how does the mitotic apparatus act to organize the contractile ring? It has been suggested that the mitotic apparatus acts to modulate locally the force generated by the cortical contractile filaments. The resultant gradients of cortical tension cause filaments to be pulled into regions of higher tension. The geometry of the stimulus from the mitotic apparatus is such that the highest levels of tension occur in the equatorial regions. The geometric distortions that take place when contractile filaments are pulled into this region cause them to become partially oriented circumferentially. When furrowing commences, mechanical forces act to align the filaments further and concentrate them in a narrow band. The furrow therefore becomes self-sharpening. Similar lateral flows of contractile filaments may occur during cell locomotion and growth cone extension.

Amphibians↗
PubMed1996

Mobility of hAT transposable elements in the Old World bollworm, Helicoverpa armigera.

The P, hobo, Hermes, Minos and mariner transposable elements have been successfully used as gene vectors to achieve genetic transformation of Drosophila melanogaster. The hobo transposable element of D. melanogaster, a member of the hAT family of transposable elements, can also transpose in other dipteran species including the house fly Musca domestica and the Queensland fruit fly, Bactrocera tryoni. Another hAT element, Hermes, can also transpose in a wide range of insect species. We report here that both of these hAT elements are also capable of mobility and accurate transposition in the noctuid Helicoverpa armigera and thus may be able to be used as gene vectors that will enable the genetic transformation of this important pest species. Significantly, the ability of hobo to excise in this species is independent of the presence of an exogenous source of hobo transposase, which suggests that H. armigera may possess an endogenous hobo-like transposable element.

Animals↗
PubMed2002

Inductively coupled plasma mass spectrometry with on-line leaching: a method to assess the mobility and fractionation of elements.

A new technique has been developed to assess the mobility and site of specific elements in complex natural materials such as rocks. Concentration profiles during leaching were obtained by pumping reagents (water, 1% HNO3, 10% HNO3, 30% HNO3), either continuously or with flow injection, through a microcolumn of sample while continuously monitoring analyte signals by inductively coupled plasma mass spectrometry (ICPMS). Compared to batch extraction procedures normally used, the approach involves minimal sample preparation and reduced contamination since the leaching is performed in a closed system. Continuous on-line monitoring also allows a greater resolution of the various phases reacting with given reagent. Compared to continuous leaching, flow injection increased the resolution of the various phases using discrete injections of reagents while reducing reagent consumption and minimizing etching of the MS interface. Furthermore, sensitivity was preserved by injecting into air instead of an aqueous carrier. Whether in the continuous or flow injection modes, the proposed approach provides real-time data on what phases are breaking down and what metals are released. It can therefore be used to design effective leaching strategies and to trace isotopic compositions. However, the resulting spectra are complex and the correct determination of some elements requires high-resolution ICPMS.

Elements↗
PubMed1996

[Analysis of motifs of functional MDG2 sites in assuring its possible molecular functions].

We analyzed the location and possible interaction of motifs of functional sites in a DNA sequence of MDG2 (Dm412) revealed by means of computer context analysis. It was shown that motifs of functional sites in the appropriate location can ensure the basic molecular functions of MDG2: expression of its ORF, transcription, induction of transposition, modification of adjacent genes and polygenes, etc. MDG2 ILTR does not contain the NTCAGTYN motif required for initiation of transcription by RNA polymerase II in the absence of the TATA box and located close to the transcription start site in most gypsy-like retrotransposons of Drosophila. Therefore, MDG2 ILTR appears to contain the classic promoter region for RNA polymerase II, contrary to other retrotransposons of the gypsy group. Enhancers of mobile genetic elements are assumed to determine modification of adjacent genes and polygenes. Excisions and transpositions of mobile elements seem to be induced by external stress factors or physiological factors through a heat-shock system.

Enhancer Elements, Genetic↗
PubMed2002

[Longevity of Drosophila after exposure to low doses of radiation and etoposide].

The review of perennial researches of the authors on a problem of radiation-induced aging is presented. From the point of view of radiogenetics it is represented perspective to investigate influence of an exogenous irradiating in small doses on fruit fly with defined mutation by phenotypes, that allows to repute a role of separate genes and mechanisms, controlled by them, in a determination of lifetime. At lines described by differences in pattern of mobile genetical elements, the different reaction to an irradiating explained from the point of view of features of the given mobile elements is found. The processing etoposide in concentration 5 microM on preimaginal stages of line with defects of a reparation (mei-41D5) and hypersensibility to an induction apoptosis (wg1-7, wg7L74, th1 [symbol: see text] th4) results in down-stroke of lifetime. The dominant effect of a gene mei-41D5 in a regulation of etoposide-induced change of lifetime is found. Is exhibited, that at lines with defects proapoptosis of genes reaper and Dcp1, the lifetime after influence, both ionizing irradiating, and inducer apoptosis etoposide is enlarged in comparison with the control.

Animals↗