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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↗
PubMed2005

Mobile genetic elements: the agents of open source evolution.

Horizontal genomics is a new field in prokaryotic biology that is focused on the analysis of DNA sequences in prokaryotic chromosomes that seem to have originated from other prokaryotes or eukaryotes. However, it is equally important to understand the agents that effect DNA movement: plasmids, bacteriophages and transposons. Although these agents occur in all prokaryotes, comprehensive genomics of the prokaryotic mobile gene pool or 'mobilome' lags behind other genomics initiatives owing to challenges that are distinct from cellular chromosomal analysis. Recent work shows promise of improved mobile genetic element (MGE) genomics and consequent opportunities to take advantage - and avoid the dangers - of these 'natural genetic engineers'. This review describes MGEs, their properties that are important in horizontal gene transfer, and current opportunities to advance MGE genomics.

Conjugation, Genetic↗
PubMed2005

Heavy metals stimulate human LINE-1 retrotransposition.

L1 and Alu elements are among the most active retroposons (mobile elements) in the human genome. Several human diseases, including certain forms of breast cancer and leukemia, are associated with L1 and Alu insertions in functionally important areas of the genome. We present data demonstrating that environmental pollutants, such as heavy metals, can stimulate L1 retrotransposition in a tissue culture system using two different types of assays. The response to these agents was equivalent when using a cell line with a stably integrated L1 vector (genomic) or a by introducing the L1 vector by transient transfection (episomal) of the cell. Reproducible results showed that mercury (HgS), cadmium (CdS), and nickel (NiO) increase the activity of L1 by an average of three (3) fold p<0.001. This observation is the first to link several carcinogenic agents with the increased retrotransposition activity of L1 as an alternate mechanism of generating genomic instability contributing to the process of carcinogenesis. Our results demonstrate that mobile element activation must be considered as one of the mechanisms when evaluating genomic damage/instability in response to environmental agents.

Animals↗
PubMed1984

Functional characterization of the prokaryotic mobile genetic element IS26.

IS26L and IS26R are the 820 bp long elements found as direct repeats at both ends of the kanamycin resistance transposon Tn2680. They can mediate cointegration in E. coli K12 which contains no IS26 in its chromosome. Cointegration occurs in rec+ or recA- strains with similar frequency. Upon cointegration mediated by either IS26R or IS26L, the element is duplicated and integrated into one of many different sites. Both IS26L and IS26R carry 14 bp perfect terminal inverted repeats and generate 8 bp direct repeats at their target sequences. Deletion formation mediated by IS26R was also observed. These functional and structural features of IS26 are characteristic of a prokaryotic mobile genetic element.

Base Sequence↗
PubMed1986

Mitochondrial introns as mobile genetic elements: the role of intron-encoded proteins.

Introns of organelle genes share distinctive RNA secondary structures that allow their classification into two known families. These structures are believed to play an essential role in splicing, and members of both structural classes have recently been shown to perform self-splicing reactions in vitro. In lower eukaryotes, many structured introns also contain long internal open reading frames (ORFs), which are able to code for hydrophilic proteins. Several properties of self-splicing structured introns suggest that they resemble mobile genetic elements, even though no actual transposition event involving these introns has yet been found. We report here on the characterization of two intron-encoded proteins that strongly support this attractive idea. First, we show that the class I intron of the 21S ribosomal RNA (rRNA) gene of Saccharomyces cerevisiae omega+ strains (rl intron) encodes a specific transposase. This protein has been partially purified from Escherichia coli cells that overexpress it from an artificial universal code equivalent to the rl intronic ORF. The omega transposase shows a double-strand endonuclease activity in vitro. This activity creates a 4-bp staggered cut with 3' OH overhangs within a specific sequence of the 21S rRNA gene of omega- strains. It is precisely within this sequence that the rl intron inserts by a duplicative transposition. Second, we report on the synthesis, in E. coli, of a putative reverse transcriptase encoded by the class II intron of the cytochrome b gene of Schizosaccharomyces pombe. This synthesis was obtained from E. coli expression vectors, using the class II intronic ORF linked to an artificial initiator sequence. As further support of the idea that structured introns are mobile, we show, from a systematic screening of introns in various yeast species, that the rl intron has transposed into the ATPase subunit 9 gene of Kluyveromyces fragilis. Structural features observed at the new intron homing site may be relevant to the transposition event.

Adenosine Triphosphatases↗
PubMed2002

The food safety perspective of antibiotic resistance.

Bacterial antimicrobial resistance in both the medical and agricultural fields has become a serious problem worldwide. Antibiotic resistant strains of bacteria are an increasing threat to animal and human health, with resistance mechanisms having been identified and described for all known antimicrobials currently available for clinical use. There is currently increased public and scientific interest regarding the administration of therapeutic and sub-therapeutic antimicrobials to animals, due primarily to the emergence and dissemination of multiple antibiotic resistant zoonotic bacterial pathogens. This issue has been the subject of heated debates for many years, however, there is still no complete consensus on the significance of antimicrobial use in animals, or resistance in bacterial isolates from animals, on the development and dissemination of antibiotic resistance among human bacterial pathogens. In fact, the debate regarding antimicrobial use in animals and subsequent human health implications has been going on for over 30 years, beginning with the release of the Swann report in the United Kingdom. The latest report released by the National Research Council (1998) confirmed that there were substantial information gaps that contribute to the difficulty of assessing potential detrimental effects of antimicrobials in food animals on human health. Regardless of the controversy, bacterial pathogens of animal and human origin are becoming increasingly resistant to most frontline antimicrobials, including expanded-spectrum cephalosporins, aminoglycosides, and even fluoroquinolones. The lion's share of these antimicrobial resistant phenotypes is gained from extra-chromosomal genes that may impart resistance to an entire antimicrobial class. In recent years, a number of these resistance genes have been associated with large, transferable, extra-chromosomal DNA elements, called plasmids, on which may be other DNA mobile elements, such as transposons and integrons. These DNA mobile elements have been shown to transmit genetic determinants for several different antimicrobial resistance mechanisms and may account for the rapid dissemination of resistance genes among different bacteria. The increasing incidence of antimicrobial resistant bacterial pathogens has severe implications for the future treatment and prevention of infectious diseases in both animals and humans. Although much scientific information is available on this subject, many aspects of the development of antimicrobial resistance still remain uncertain. The emergence and dissemination of bacterial antimicrobial resistance is the result of numerous complex interactions among antimicrobials, microorganisms, and the surrounding environments. Although research has linked the use of antibiotics in agriculture to the emergence of antibiotic-resistant foodborne pathogens, debate still continues whether this role is significant enough to merit further regulation or restriction.

Animal Husbandry↗
PubMed2003

Towards a genotyping system for Streptococcus agalactiae (group B streptococcus): use of mobile genetic elements in Australasian invasive isolates.

This study forms part of the development of an integrated genotyping system for Streptococcus agalactiae (group B streptococcus, GBS) that can be used to study the population genetics of the organism and the pathogenesis and epidemiology of GBS disease. In recent previous studies, two sets of markers, the capsular polysaccharide synthesis (cps) gene cluster and surface protein antigen genes, have been used to assign molecular serotypes (MS) and protein-gene profiles (PGP) to more than 200 isolates. In the present study, five mobile genetic elements (MGE) have been used as a third set of markers, to characterize further 194 invasive isolates, recovered from blood or cerebrospinal fluid (CSF). Of these, 97 % contained one or more of the five MGE, the distribution of which was related to MS and PGP, as illustrated by MS III, which is divisible into four serosubtypes with different combinations of the MGE (or none). Fifty-six different genotypes and eight genetic clusters were identified, each with different combinations of the three sets of molecular markers. Five predominant genotypes (Ia-1, Ib-1, III-1, III-2 and V-1) contained 62 % of the isolates and five of the eight genetic clusters contained 92 % of the isolates. The 17 CSF isolates were relatively widely distributed between 10 genotypes and across seven of the eight clusters. Further study is needed to determine whether these genotypes or clusters share common markers of increased virulence. In future, comparison of invasive with colonizing strains of GBS may elucidate the significance of these findings.

Adolescent↗
PubMed2001

Gene duplication and mobile genetic elements in the morning glories.

We review gene duplication and subsequent structural and functional divergence in the anthocyanin biosynthesis genes in the Japanese and common morning glories and discuss their evolutionary implications. These plants appear to contain at least six copies of the CHS gene and three tandem copies of the DFR gene. Of these, the CHS-D and DFR-B genes are mainly responsible for flower pigmentation and mutations in these genes confer white flowers. We compared the genomic sequences of these duplicated genes between the two morning glories and found small mobile element-like sequences (MELSs) and direct repeats (DRs) in introns and intergenic regions. The results indicate that the MELS elements and DRs play significant roles in divergence after gene duplication. We also discuss DNA rearrangements occurring before and after speciation of these morning glories. DNA transposable elements belonging to the Ac/Ds or En/Spm families have acted as major spontaneous mutagens in these morning glories. We also describe the structural features of the first Mu-related element found in the morning glories and polymorphisms found in the same species.

Alcohol Oxidoreductases↗
PubMed1992

Induction of the mobile genetic element Dm-412 transpositions in the Drosophila genome by heat shock treatment.

Males of a Drosophila melanogaster isogenic line with a mutation of the major gene for radius incompletus (ri) were treated by standard light heat shock (37 degrees C for 90 min) and by heavy heat shock (transfer of males from 37 degrees C for 2 hr to 4 degrees C for 1 hr and back; this procedure was repeated three times). In the F1 generation of treated males mated with nontreated females of the same isogenic line, mass transpositions of copia-like mobile genetic element Dm-412 were found. The altered positions of the element seem nonrandom; five "hot spots" of transposition were found. Probabilities of transpositions were estimated after light heat shock and heavy heat shock and in the control sample. These probabilities were, respectively, 3.4 x 10(-2), 8.7 x 10(-2), and less than 4.1 x 10(-4) transpositions per genome per occupied position per generation. Therefore, as a result of heat shock treatment, the probabilities of transpositions were two orders of magnitude greater than those of the control sample in the next generation after induction. Comparison of the results with those after stepwise temperature treatment shows that the induction depends on the intensity of the stress action (temperature treatment) rather than on the type of the stress action.

Animals↗
PubMed1994

IS1237, a repetitive chromosomal element from Clavibacter xyli subsp. cynodontis, is related to insertion sequences from gram-negative and gram-positive bacteria.

We describe here a repetitive chromosomal element, which appears to be an insertion sequence, isolated from Clavibacter xyli subsp. cynodontis, a gram-positive plant-associated bacterium. The element, IS1237, is 905 bp in size, is bounded by 19-bp perfect inverted repeats and 3-bp direct repeats, and appears at least 16 times in the genome. It contains three open reading frames which show similarity to open reading frames from various other insertion sequences. We have found that there are two groups of related mobile elements: one in which two open reading frames are read separately and the other in which these two open reading frames are fused together to give one predicted protein product. Using one of these open reading frames to search amino acid sequence databases, we found two instances in which similar reading frames flank genes carried on plasmids. We believe therefore that these plasmid-borne genes may be parts of previously unidentified mobile elements. For IS1237, a frameshift in two of the open reading frames and a stop codon in the third may indicate that this particular copy of the element is no longer active in transposition. The similarity of IS1237 to other elements from both gram-negative and gram-positive bacteria provides further evidence that mobile elements have been transferred between these two bacterial groups.

Actinomycetales↗
PubMed1999

Evolution of tandemly repeated sequences: What happens at the end of an array?

Tandemly repeated sequences are a major component of the eukaryotic genome. Although the general characteristics of tandem repeats have been well documented, the processes involved in their origin and maintenance remain unknown. In this study, a region on the paternal sex ratio (PSR) chromosome was analyzed to investigate the mechanisms of tandem repeat evolution. The region contains a junction between a tandem array of PSR2 repeats and a copy of the retrotransposon NATE, with other dispersed repeats (putative mobile elements) on the other side of the element. Little similarity was detected between the sequence of PSR2 and the region of NATE flanking the array, indicating that the PSR2 repeat did not originate from the underlying NATE sequence. However, a short region of sequence similarity (11/15 bp) and an inverted region of sequence identity (8 bp) are present on either side of the junction. These short sequences may have facilitated nonhomologous recombination between NATE and PSR2, resulting in the formation of the junction. Adjacent to the junction, the three most terminal repeats in the PSR2 array exhibited a higher sequence divergence relative to internal repeats, which is consistent with a theoretical prediction of the unequal exchange model for tandem repeat evolution. Other NATE insertion sites were characterized which show proximity to both tandem repeats and complex DNAs containing additional dispersed repeats. An "accretion model" is proposed to account for this association by the accumulation of mobile elements at the ends of tandem arrays and into "islands" within arrays. Mobile elements inserting into arrays will tend to migrate into islands and to array ends, due to the turnover in the number of intervening repeats.

Base Sequence↗
PubMed2004

Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome overrun by mobile genetic elements.

The complete sequence of the 1,267,782 bp genome of Wolbachia pipientis wMel, an obligate intracellular bacteria of Drosophila melanogaster, has been determined. Wolbachia, which are found in a variety of invertebrate species, are of great interest due to their diverse interactions with different hosts, which range from many forms of reproductive parasitism to mutualistic symbioses. Analysis of the wMel genome, in particular phylogenomic comparisons with other intracellular bacteria, has revealed many insights into the biology and evolution of wMel and Wolbachia in general. For example, the wMel genome is unique among sequenced obligate intracellular species in both being highly streamlined and containing very high levels of repetitive DNA and mobile DNA elements. This observation, coupled with multiple evolutionary reconstructions, suggests that natural selection is somewhat inefficient in wMel, most likely owing to the occurrence of repeated population bottlenecks. Genome analysis predicts many metabolic differences with the closely related Rickettsia species, including the presence of intact glycolysis and purine synthesis, which may compensate for an inability to obtain ATP directly from its host, as Rickettsia can. Other discoveries include the apparent inability of wMel to synthesize lipopolysaccharide and the presence of the most genes encoding proteins with ankyrin repeat domains of any prokaryotic genome yet sequenced. Despite the ability of wMel to infect the germline of its host, we find no evidence for either recent lateral gene transfer between wMel and D. melanogaster or older transfers between Wolbachia and any host. Evolutionary analysis further supports the hypothesis that mitochondria share a common ancestor with the alpha-Proteobacteria, but shows little support for the grouping of mitochondria with species in the order Rickettsiales. With the availability of the complete genomes of both species and excellent genetic tools for the host, the wMel-D. melanogaster symbiosis is now an ideal system for studying the biology and evolution of Wolbachia infections.

Adenosine Triphosphate↗
PubMed2004

Pathogenomics of mobile genetic elements of toxigenic bacteria.

The growing knowledge of genetic diversity and whole genome organization in bacteria shows that pathogenicity islands (PAIs) represent a subtype of a more general genetic element, termed genomic island (GEI), which is widespread among pathogenic and non-pathogenic microbes. These findings mirror the importance of horizontal gene transfer, genome reduction and recombination events as fundamental mechanisms involved in evolution of bacterial variants. GEIs are part of the flexible gene pool and carry selfish genes, but also determinants which may be beneficial under certain conditions thus increasing bacterial fitness and consequently their survival or transmission. In this review, we focus on the role of mobile genetic elements that may also contain toxin-encoding genes for genome variability and evolution of bacteria.

Bacterial Toxins↗
PubMed2003

Complete nucleotide sequence of pHG1: a Ralstonia eutropha H16 megaplasmid encoding key enzymes of H(2)-based ithoautotrophy and anaerobiosis.

The self-transmissible megaplasmid pHG1 carries essential genetic information for the facultatively lithoautotrophic and facultatively anaerobic lifestyles of its host, the Gram-negative soil bacterium Ralstonia eutropha H16. We have determined the complete nucleotide sequence of pHG1. This megaplasmid is 452,156 bp in size and carries 429 potential genes. Groups of functionally related genes form loose clusters flanked by mobile elements. The largest functional group consists of lithoautotrophy-related genes. These include a set of 41 genes for the biosynthesis of the three previously identified hydrogenases and of a fourth, novel hydrogenase. Another large cluster carries the genetic information for denitrification. In addition to a dissimilatory nitrate reductase, both specific and global regulators were identified. Also located in the denitrification region is a set of genes for cytochrome c biosynthesis. Determinants for several enzymes involved in the mineralization of aromatic compounds were found. The genes for conjugative plasmid transfer predict that R.eutropha forms two types of pili. One of them is related to the type IV pili of pathogenic enterobacteria. pHG1 also carries an extensive "junkyard" region encompassing 17 remnants of mobile elements and 22 partial or intact genes for phage-type integrase. Among the mobile elements is a novel member of the IS5 family, in which the transposase gene is interrupted by a group II intron.

Anaerobiosis↗
PubMed1994

[Effect of heat shock on transpositions of Mobile Genetic Element Dm412 in three isogenetic lines of Drosophila melanogaster].

Induction of Dm412 transpositions by heavy heat shock was studied in several isogenic lines of Drosophila melanogaster. The probabilities of spontaneous and induced transpositions were estimated. Their respective values were less than < 3.0 x 10(-3) and 3.8 x 10(-2) per site per genome per generation in line 51, and less than < 3.6 x 10(-3) and 2.6 x 10(-2) in line 66. These estimates are close to those obtained earlier for Dm412 (less than < 3.3 x 10(-4) and 7.2 x 10(-2) and for B104, line 49 (less than < 1.7 x 10(-3) and 8.1 x 10(-2)). Thus, transposition induction of copia-like mobile genetic elements by heavy heat shock is a general phenomenon common for various isogenic lines of Drosophila. Other properties of Dm412 and B104 transpositions, such as the presence of "hot" and "cold" sites, HSI haplotypes etc., are also similar.

Animals↗
PubMed2004

Large plasmid pCAR2 and class II transposon Tn4676 are functional mobile genetic elements to distribute the carbazole/dioxin-degradative car gene cluster in different bacteria.

The carbazole-catabolic plasmid pCAR1 isolated from Pseudomonas resinovorans strain CA10 was sequenced in its entirety; and it was found that pCAR1 carries the class II transposon Tn4676 containing carbazole-degradative genes. In this study, a new plasmid designated pCAR2 was isolated from P. putida strain HS01 that was a transconjugant from mating between the carbazole-degrader Pseudomonas sp. strain K23 and P. putida strain DS1. Southern hybridization and nucleotide sequence analysis of pCAR1 and pCAR2 revealed that the whole backbone structure was very similar in each. Plasmid pCAR2 was self-transmissible, because it was transferred from strain HS01 to P. fluorescens strain IAM12022 at the frequency of 2 x 10(-7) per recipient cell. After the serial transfer of strain HS01 on rich medium, we detected the transposition of Tn4676 from pCAR2 to the HS01 chromosome. The chromosome-located copy of Tn4676 was flanked by a 6-bp target duplication, 5'-AACATC-3'. These results experimentally demonstrated the transferability of pCAR2 and the functionality of Tn4676 on pCAR2. It was clearly shown that plasmid pCAR2 and transposon Tn4676 are active mobile genetic elements that can mediate the horizontal transfer of genes for the catabolism of carbazole.

Bacterial Proteins↗
PubMed2002

Bacterial group II introns and their association with mobile genetic elements.

Group II introns are an abundant class of self-splicing RNAs, found primarily in the organelles of plants and lower eukaryotes and in bacteria. The first bacterial group II intron identified to be functional for splicing in vivo was the Ll.ltrB intron of Lactococcus lactis. It has served as an excellent model for the study of group II intron structure and function. Taking advantage of the tools of bacterial genetics and biochemical methodologies, details of Ll.ltrB splicing and homing reactions have been elucidated and are similar to those of fungal group II introns. This review provides a summary of these results. Of particular interest is the potential use of Ll.ltrB as an agent for targeted gene disruption. In addition, the development of a genetic system to analyze Ll.ltrB splicing promises to provide new insight into group II intron structure and function. Identification and analysis of group II introns in other bacterial species is a continuing process, and a discussion of published reports on these introns is provided here. Limited functional data is available for most of these introns, but sequence analysis points out several common themes, most notably that bacterial group II introns are almost always carried on mobile genetic elements.

Base Sequence↗
PubMed1993

Doc and copia instability in an isogenic Drosophila melanogaster stock.

A high degree of heterogeneity and an overall increase in number of insertion sites of the mobile elements Doc and copia were revealed in one substock of an isogenic Drosophila melanogaster stock, while in two other substocks the distribution of copia sites was highly homogenous, but that of Doc sites was again heterogeneous. We therefore concluded that copia was unstable in one of the substocks and Doc was unstable in all. Doc instability presumably arose earlier than copia instability. Doc and copia transpositions were directly observed in experiments with one substock. An abundance of copia insertions was revealed in the X chromosome where insertions with deleterious effects are exposed to selection in hemizygous condition. The locations of many other mobile elements (mdg1, mdg2, mdg3, mdg4, 297, B104, H.M.S. Beagle, I, P, BS, FB) were found to be conserved in each substock and did not differ between them, indicating that these mobile elements were stable. This homogeneity is a strong argument against any possibility of inadvertent contamination.

Animals↗