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Results for “Interspersed Repetitive Sequences”

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PubMed2005

The promiscuous primase.

DNA primases are essential for the initiation of DNA replication and progression of the replication fork. Recent phylogenetic analyses coupled with biochemical and structural studies have revealed that the arrangement of catalytic residues within the archaeal and eukaryotic primase has significant similarity to those of the Pol X family of DNA-repair polymerases. Furthermore, two additional groups of enzymes, the ligase/primase of the bacterial nonhomologous end-joining machinery and a putative replicase from an archaeal plasmid have shown striking functional and structural similarities to the core primase. The promiscuous nature of the archaeal primases suggests that these proteins might have additional roles in DNA repair in the archaea.

Catalytic Domain↗

PubMed2006

I am what I eat and I eat what I am: acquisition of bacterial genes by giant viruses.

Giant viruses are nucleocytoplasmic large DNA viruses (NCLDVs) that infect algae (phycodnaviruses) and amoebae (Mimivirus). We report an unexpected abundance in these giant viruses of islands of bacterial-type genes, including apparently intact prokaryotic mobile genetic elements, and hypothesize that NCLDV genomes undergo successive accretions of bacterial genes. The viruses could acquire bacterial genes within their bacteria-feeding eukaryotic hosts, and we suggest that such acquisition is driven by the intimate coupling of recombination and replication in NCLDVs.

Chromosome Mapping↗

PubMed2004

Horizontal gene transfer and microbial adaptation to xenobiotics: new types of mobile genetic elements and lessons from ecological studies.

The characterization of bacteria that degrade organic xenobiotics has revealed that they can adapt to these compounds by expressing 'novel' catabolic pathways. At least some of them appear to have evolved by patchwork assembly of horizontally transmitted genes and subsequent mutations and gene rearrangements. Recent studies have revealed the existence of new types of xenobiotic catabolic mobile genetic elements, such as catabolic genomic islands, which integrate into the chromosome after transfer. The significance of horizontal gene transfer and patchwork assembly for bacterial adaptation to pollutants under real environmental conditions remains uncertain, but recent publications suggest that these processes do occur in a polluted environment.

Adaptation, Physiological↗

PubMed2004

Quantitative PCR for DNA identification based on genome-specific interspersed repetitive elements.

We have designed and evaluated a series of class-specific (Aves), order-specific (Rodentia), and species-specific (equine, canine, feline, rat, hamster, guinea pig, and rabbit) polymerase chain reaction (PCR)-based assays for the identification and quantitation of DNA using amplification of genome-specific short and long interspersed elements. Using SYBR Green-based detection, the minimum effective quantitation levels of the assays ranged from 0.1 ng to 0.1 pg of starting DNA template. Background cross-amplification with DNA templates derived from sixteen other species was negligible prior to 30 cycles of PCR. The species-specificity of the PCR amplicons was further demonstrated by the ability of the assays to accurately detect known quantities of species-specific DNA from mixed (complex) sources. The 10 assays reported here will help facilitate the sensitive detection and quantitation of common domestic animal and bird species DNA from complex biomaterials.

Animals↗

PubMedDate not supplied

Trypanosoma brucei: trypanosome strain typing using PCR analysis of mobile genetic elements (MGE-PCR).

We describe the development of a single-primer amplification system, which uses the trypanosomal mobile genetic element RIME as a molecular marker for the differentiation of Trypanosoma brucei stocks. Using a well-characterised set of T. brucei stocks from southeast Uganda, Kenya and Zambia, we have evaluated the application of this technique, termed MGE-PCR (mobile genetic element PCR) for the typing of trypanosome strains. The technique revealed considerable variation between stocks and was sufficiently specific to amplify trypanosomal DNA in the presence of host DNA. The results showed a clear distinction between human-infective and non-human-infective stocks. Comparative studies on these stocks using markers for the human serum resistance associated (SRA) gene, which identifies human-infective stocks, demonstrated complete agreement between MGE-PCR derived groups and human-infectivity status. Furthermore, MGE-PCR detects high levels of variability within the T. b. brucei and T. b. rhodesiense groups and is therefore a powerful discriminatory tool for tracking individual T. brucei genotypes and strains.

Animals↗

PubMed2001

Use of mobile genetic elements as tools for molecular epidemiology.

Trypanosomiasis is a complex zoonotic disease where human-infective and non-human-infective strains of Trypanosoma brucei interact in the same transmission cycles. Differentiating these strains is paramount to understanding disease epidemiology. Restriction fragment length polymorphism analysis of repetitive DNA has provided such a method for distinguishing human and non-human isolates. Unfortunately, this approach requires large amounts of material and a more rapid approach is required. We have developed a novel technique, mobile genetic element-PCR, for assaying for positional variation of the mobile genetic element, RIME. The trypanosome genome contains up to 400 copies of RIME. Using this approach we have observed considerable variation between strains of T. brucei. Such a technique may offer potential as a method for differentiating non-human- and human-infective trypanosomes and shows promise as a rapid sensitive tool for investigating the epidemiology of sleeping sickness.

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↗

PubMed1998

Genetic organization of the regions associated with surface polysaccharide synthesis in Vibrio cholerae O1, O139 and Vibrio anguillarum O1 and O2: a review.

Vibrio cholerae and V. anguillarum are recognized as aquatic-borne human and fish pathogens, respectively. Based upon analyses of several genes and the presence of novel genetic elements it seems that these two species are very closely related. Studies in this laboratory have identified an association of IS1358 with rfb and capsule loci in these two species. The most recent findings suggest that IS1358 is associated with the rfb region in V. cholerae O1 and O139 and in V. anguillarum O1 and O2. In addition, the rfb region in both V. cholerae serogroups and in V. anguillarum O1 is limited at one end by gmhD. These features make it feasible to envisage a mechanism by which the evolution of new rfb genes is taking place involving IS1358 and the region around gmhD. Furthermore, it is possible to envisage that there is or has been an exchange of genetic material between these species leading to new rfb/capsule regions. This review examines the genetics and biosynthesis of the O-antigen and capsule of V. cholerae O1 and O139, as well as the V. anguillarum serogroup O1 and the role of IS1358. Throughout this review we have used the new nomenclature for rfb genes proposed by.

Bacterial Proteins↗

PubMed2003

The role of mobile genetic elements in bacterial adaptation to xenobiotic organic compounds.

Retrospective studies clearly indicate that mobile genetic elements (MGEs) play a major role in the in situ spread and even de novo construction of catabolic pathways in bacteria, allowing bacterial communities to rapidly adapt to new xenobiotics. The construction of novel pathways seems to occur by an assembly process that involves horizontal gene transfer: different appropriate genes or gene modules that encode different parts of the novel pathway are recruited from phylogenetically related or distant hosts into one single host. Direct evidence for the importance of catabolic MGEs in bacterial adaptation to xenobiotics stems from observed correlations between catabolic gene transfer and accelerated biodegradation in several habitats and from studies that monitor catabolic MGEs in polluted sites.

Adaptation, Physiological↗

PubMed1998

Mobile elements and disease.

A substantial fraction of mammalian genomes is composed of mobile elements and their remnants. Recent insertions of LTR-retrotransposons, non-LTR retrotransposons, and non-autonomous retrotransposons have caused disease frequently in mice, but infrequently in humans. Although many of these elements are defective, a number of mammalian non-LTR retrotransposons of the L1 type are capable of autonomous retrotransposition. The mechanism by which they retrotranspose and in turn aide the retrotransposition of non-autonomous elements is being elucidated.

Animals↗

PubMed1999

Shaping the genome--restriction-modification systems as mobile genetic elements.

A restriction enzyme gene is often linked to a modification methylase gene the role of which is to protect a recognition site on DNA from breakage by the former. Loss of some restriction-modification gene complexes leads to cell death through restriction breakage in the genome. Their behavior as genomic parasites/symbionts may explain the distribution of restriction sites and clarify certain aspects of bacterial recombination repair and mutagenesis. A comparison of bacterial genomes supports the hypothesis that restriction-modification gene complexes are mobile elements involved in various genome rearrangements and evolution.

Bacteria↗

PubMed1999

Genotyping of Actinobacillus actinomycetemcomitans serotype d isolates based on polymerase chain reaction.

The aims of the study were to determine the genetic diversity of the rare Actinobacillus actinomycetemcomitans serotype d and to compare the ability of the repetitive extragenic palindromic element (REP)-based polymerase chain reaction (PCR) with that of the arbitrarily primed (AP)-PCR to discriminate between and within A. actinomycetemcomitans serotypes. The material included 26 A. actinomycetemcomitans serotype d isolates, 3 reference strains, and 21 A. actinomycetemcomitans isolates, representing the previously described 17 AP-PCR genotypes from 4 serotypes (a, b, c and e). Among A. actinomycetemcomitans serotype d isolates (n = 26), the AP-PCR primer distinguished 2 genotypes, whereas the REP-primer pair (REP1R-I and REP2-I) and the (GACA)4 primer each produced one genotype. Among the total of 50 A. actinomycetemcomitans isolates, REP-primer pair distinguished 6 genotypes, the primer (GACA)4 7 genotypes, and the AP-PCR 19 genotypes. Among A. actinomycetemcomitans serotype a isolates (n = 6), REP-primer pair yielded 3 genotypes and (GACA)4 and AP-PCR primer 4 genotypes, and among serotype e isolates (n = 6) 3 genotypes. All serotype b isolates (n = 7), representing the AP-PCR genotypes 2, 9, 8, 12, 13, 16 and serotype c isolates (n = 5), AP-PCR genotypes 3, 4, 14, 15, belonged to the (REP1R-I and REP2-I)-PCR genotype 4 and to the (GACA)4-PCR genotype 4. In conclusion, based on both the AP-PCR method and the less discriminative REP-PCR methods, the present genotyping results indicated limited genetic diversity among serotype d isolates of A. actinomycetemcomitans.

Aggregatibacter actinomycetemcomitans↗

PubMed2000

Mobile elements and the human genome.

Genomic DNA is often thought of as the stable template of heredity, largely dormant and unchanging, apart from perhaps the occasional point mutation. But it has become increasingly clear that DNA is dynamic rather than static, being subjected to rearrangements, insertions and deletions. Much of this plasticity can be attributed to transposable elements and their genomic relatives.

Biotechnology↗

PubMed2001

The role of selfish genetic elements in eukaryotic evolution.

'Selfish genetic elements', such as transposons, homing endonucleases, meiotic drive chromosomes and heritable microorganisms, are common features of eukaryotes. However, their importance in the evolution of eukaryotic genomes is still controversial. In this review, we discuss these diverse elements and their potential importance in the evolution of genetic systems, adaptation, and the extinction and birth of species.

Animals↗

PubMed2000