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PubMed1998

Mobile genetic elements, chiasmata, and the unique organization of beta-heterochromatin.

Beta-heterochromatin in Drosophila and the Syrian hamster share a similar DNA organization, few unique sequences, and scrambled repeats of mobile elements without tandem repetition. DNA in alpha-heterochromatin is tandemly repetitious, and we now show that the repeat unit can either contain or lack a mobile element. The tandem repeat organization of alpha-heterochromatin is presumably due to a concertina-like mechanism of unequal exchange between repeat units. Although both heterochromatin types are late replicating and can incorporate mobile retroposons, the sequence distinction between the two heterochromatins appears to be due to a property conferred by chiasmata upon the process of homologous recombination in beta-heterochromatin but not in alpha-heterochromatin. Chiasmata seem to suppress the concertina mechanism of unequal exchange and impart to beta-heterochromatin its nontandem, scrambled repeat organization.

Animals↗
PubMed1986

Concerted transpositions of mobile genetic elements coupled with fitness changes in Drosophila melanogaster.

In an inbred low-activity (LA) strain of Drosophila melanogaster with a low level of fitness and a complex of inadaptive characters, in situ hybridization reveals an invariant pattern of distribution of three copia-like elements (mdg-1, mdg-3, and copia). Rare, spontaneous, multiple transpositions of mobile elements in the LA strain were shown to be coupled with a drastic increase of fitness. A changed pattern of various types of mobile elements was also observed on selecting the LA strain for higher fitness. High-fitness strains show transpositions of mobile elements to definite chromosomal sites ("hot spots"). Concerted changes in the location of three different mobile elements were found to be coupled with an increase of fitness. The mdg-1 distribution patterns were also examined in two low-fitness strains independently selected from the high-fitness ones. Fitness decrease was accompanied by mdg-1 excision from the hot spots of their location usually detected in the high-fitness strains. The results suggest the existence of a system of adaptive transpositions of mobile elements that takes part in fitness control.

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↗
PubMed1995

[Endogenous cellular reverse transcriptase in the rat brain. A comparative analysis of the authentic enzyme and recombinant reverse transcriptase coded by a mobile genetic element of the LINE class].

A purified preparation of endogenous RNA-dependent DNA-polymerase (reverse transcriptase) earlier identified in rat brain (Ivanov, V.A., Pakhotin, P.I., Bobkova, N.V., and Ilyin, Yu.V. parallel Dokl. RAN (1992). V. 323, P. 173-177) has been obtained. A comparative analysis of the enzyme and recombinant reverse transcriptase coded by the mobile genome element jockey earlier expressed in a heterological cell system (Ivanov V.V., Melnikov A.A., Siunov A.V., Fodor I.I., Ilyin, Yu.V. parallel EMBO J. (1991), V. 10, P. 2489-2495) has been carried out. Like retroviral RNA-dependent DNA-polymerases, these enzymes show preference for polyribonucleotides and can use poly(rCm) as template. Besides they are inhibited by SH-reagents and require bivalent cations (Mg2+ or Mn2+) and detergent and/or KCl as ionic strength carrier. The enzymes differ drastically from retrovirus reverse transcriptases by a number of catalytic properties (low optima of concentration of requisite cations and ionic strength, strong preference for Mn2+, highly efficiency in using poly(rCm), lack of associated RNase H activity) but exhibit a high degree of similarity among themselves with regard to the above properties. It is suggested that endogenous reverse transcriptase from rat brain is a product of expression of the mobile genome element of the LINE family.

Animals↗
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↗
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↗
PubMed2025

Lactococcal mobile genetic elements harbour a diverse phage defensome rich in restriction-modification systems.

The genomes of 43 distinct lactococcal strains were reconstructed by a combination of long- and short-read sequencing, resolving the plasmid complement and methylome of these strains. The genomes comprised 43 chromosomes of approximately 2.5 Mb each and 269 plasmids ranging from 2 to 211 kb (at an average occurrence of 6 per strain). A total of 953 antiphage genes representing 538 phage defence systems were identified in the 43 strains and were catalogued and cross-correlated with co-occurrent mobile elements, which indicated that almost 60% of these systems are predicted to be mobile. Detailed analysis established that restriction-modification (R-M) systems form a significant portion of this mobile phage defensome. As such, all detected Type I, II, and III-associated methylated motifs (46 of which were unique to this study) were matched to their corresponding methylating enzymes by homology detection or molecular cloning. The cumulative antiphage activity of selected systems and the ability of truncated R-M genes to contribute to methylation were demonstrated. This study reveals, for the first time, the dairy lactococcal plasmidome to be a rich reservoir of orphan HsdS-encoding genes, in a comprehensive survey of (mobile) phage defence systems in lactic acid bacteria.

Bacteriophages↗
PubMed2002

Mobile genetic element activation and genotoxic cancer therapy: potential clinical implications.

Approximately one-quarter of the human genome is composed of short and long interspersed elements (SINEs and LINEs, respectively). These elements have spread throughout the genome by a process termed retrotransposition, consisting of transcription of an element into RNA, reverse transcription into cDNA, and reinsertion of the copied element into a new genomic location. Recombination events involving these elements, including novel insertions into active genes, have been associated with a number of human diseases. Despite the fact that these elements have replicated to hundreds of thousands of copies in the genome, under most conditions they remain transcriptionally silent, and therefore are not actively replicating. The signals controlling retrotransposable element activation in the genome have not been defined. Our laboratory recently found that exposure of cells to a variety of DNA-damaging agents, including several common chemotherapeutic drugs and gamma-radiation, is associated with dramatic induction of SINE transcription, and of a concomitant endogenous reverse transcriptase activity. As SINEs do not encode for reverse transcriptase, the latter finding suggests a more global activation of retrotransposable elements in response to DNA damage. Together these observations suggest that genotoxic exposure may lead to genomic mutation not only through direct DNA damage, but also through indirect activation of potentially mutagenic mobile elements in the genome. The nonrandom distribution of retrotransposable elements in the human genome may contribute to the pattern of characteristic translocation events associated with secondary malignancies in patients exposed to genotoxic agents. Here we describe these and other mechanisms by which retrotransposable elements can contribute to disease, and present an overview of what is known about this large, and largely unexplored, segment of the genome. Understanding the cellular responses to genotoxic stress may permit the development of a means of predicting the risks and preventing the development of secondary malignancy following cancer therapy.

Antineoplastic Agents↗
PubMed2026

Interspecies Exchange of Mobile Genetic Elements During a Plant Disease Outbreak.

Outbreak sequencing provides insight into the origin and evolutionary processes acting on emerging pathogens. Sequencing a historic multihost outbreak of Ralstonia spp. in Martinique shows the outbreak was caused by two lineages that diverged at separate times from mainland populations. One lineage (Ralstonia pseudosolanacearum I-18) was originally introduced from Asia to South America, where it became well established prior to its dissemination to Martinique, where it retains a signature of specialization on solanaceous hosts. The novel lineage first identified during the outbreak (Ralstonia solanacearum IIB-4NPB) arose from a mainland population endemic to the Americas prior to its arrival in Martinique, where host-range expansion was observed. In contrast to minor changes in secreted effector protein repertoires, the emergent R. solanacearum IIB-4NPB acquired a novel integrative and conjugative element (ICERsoRUN1145). After identifying all Ralstonia spp. ICEs and mapping their spatial and phylogenetic distribution among Ralstonia spp. sampled during the outbreak, we found closely related ICEs circulating in mainland populations of R. pseudosolanacearum, indicating likely exchange between introduced and endemic Ralstonia spp. The family of ICEs in Ralstonia (ICERs) has a conserved bipartite structure and display a striking pattern of functional specialization in each cargo gene insertion hotspot: the first hotspot is a target for metabolic gene acquisition, and the second is a target for defense element acquisition. This work provides unparalleled phylogenetic and spatial resolution of an unusual outbreak and highlights the role of horizontal transfer in shaping the ecological success of an emerging pathogen.

Plant Diseases↗
PubMed1995

Mobile genetic elements of Fusobacterium nucleatum.

The gram-negative anaerobic bacterium, Fusobacterium nucleatum, is a predominant member of the human oral flora. As a major component of subgingival plaque, this bacterium has a significant impact on the ecology of the oral cavity due to its ability to adhere to many different microbial species. The objective of this study was to identify and characterize plasmids and transposons that may have the potential to be developed into tools for cloning, genetic transformation, and mutagenesis of oral isolates of F. nucleatum. Analysis of a collection of laboratory strains resulted in the identification of a homologous family of small cryptic plasmids. Plasmids within this family ranged in size from 6.0 to 6.6 kb. Eighteen percent of all strains examined (n = 74) contained DNA sequences related to the plasmids. Homologous plasmid sequences were found in strains belonging to 2 of the 3 subspecies of the bacterium. The 2 smallest plasmid species were cloned in Escherichia coli to facilitate endonuclease restriction mapping. Among the strains examined for plasmids, 5 exhibited resistance to at least 10 micrograms/ml of tetracycline. These strains, all members of the subsp. polymorphum, contained a tetracycline resistance determinant (TetM) as part of a Tn916-like integrated transposon sequence. The Tn916-like element and 1 of the plasmid species co-resided in a single strain of the bacterium. Hybridization patterns of the Tn916-like sequences were identical in all 5 tetracycline-resistant strains. However, these strains appeared to be clonally distinct based on genomic fingerprinting.

Base Sequence↗
PubMed1994

ISL2, a new mobile genetic element in Lactobacillus helveticus.

Spontaneous, phenotypically stable mutations at the beta-galactosidase locus (lacL-lacM) in Lactobacillus helveticus were identified and analyzed. We found that a significant number of mutations were caused by integration of a new IS element, ISL2, into these lac genes. ISL2 is 858 bp long, flanked by 16-bp perfect inverted repeats and generates 3-bp target duplications upon insertion. It contains one open reading frame, which shows significant homology (40.1% identity) to the putative transposase of IS702 from Cyanobacterium calothrix. ISL2 is present in 4-21 copies in the L. helveticus genome, but it is not found in other lactic acid bacteria. Its divergence in copy number and genomic locations in different L. helveticus strains makes it useful as a tool for strain identification by genetic fingerprinting.

Amino Acid Sequence↗
PubMed1995

A new mobile genetic element in Lactobacillus delbrueckii subsp. bulgaricus.

A new IS element (ISL3) was discovered in Lactobacillus delbrueckii subsp. bulgaricus during the characterization of the linkage relationships between the two genes important for milk fermentation, beta-galactosidase (lacZ) and the cell-wall associated protease (prtP). ISL3 is a 1494 bp element, flanked by 38 bp imperfect inverted repeats, and generates an 8 bp target duplication upon insertion. It contains one open reading frame, encoding a potential polypeptide of 434 amino acids, which shows significant homology (34% identity) to the transposase of the Leuconostoc mesenteroides element IS1165. Molecular analysis of spontaneous lacZ mutants revealed some strains that had sustained deletions of 7 to 30 kb in size, centered on and eliminating the copy of ISL3 next to lacZ. Other deletion endpoints were identified as located immediately adjacent to ISL3. Furthermore, genetic translocations that had occurred via transposition of ISL3 were observed fortuitously in cultures screened for deletion mutants. ISL3 can be found in one to several copies in various strains of L. delbrueckii. However, it was not present in other dairy lactic acid bacteria tested.

Amino Acid Sequence↗
PubMed1998

Retrotransposal integration of mobile genetic elements in human diseases.

Approximately one-third of the mammalian genome is composed of highly repeated DNA sequences, of which the two major families, the long and short inter-spersed nucleotide elements (LINEs and SINEs), are represented in humans by L1 and Alu elements respectively. Both 'types of element are considered to be retrotransposable and to play significant roles in genomic function and evolution. The majority of inserted elements are truncated and often rearranged relative to full-length elements; usually, such retrotransposed sequences are flanked by target-site duplications of various lengths and contain 3' polyA tracts, common characteristics of retrotransposal integration. Retrotransposal integrations of Alu and L1 sequences into biologically important genes appear to play significant roles in some human diseases. Most of the inserted sequences that cause human diseases seem to belong to one or a few subsets of each type of retrotransposon, suggesting that only a few active elements can function as templates for retrotransposition. Integrations observed in oncogenes and in tumor suppressor genes may participate in carcinogenesis by altering the activity of the affected genes. The exact mechanism of these events is unclear; however, retrotransposal integration may be a general mechanism of mutation in humans.

Animals↗
PubMed2002

Correlation of phylogenetic lineages of group B Streptococci, identified by analysis of restriction-digestion patterns of genomic DNA, with infB alleles and mobile genetic elements.

Phylogenetic lineages of pathogenic Streptococcus agalactiae (group B streptococci [GBS]) can be identified by analysis of restriction-digestion patterns (RDPs) of chromosomal DNA. The purpose of the present study was to correlate GBS RDP types and (1) alleles of the highly conserved gene encoding translation-initiation factor IF2, infB, and/or (2) the inserted elements IS1548 and GBSi1. Only 1 combination of serotype and infB allele was found within each RDP type. Strains within a particular RDP type also tend to have the same inserted elements in each of 3 loci examined. A novel insertion sequence, designated "IS1563," was found within all RDP type II-2 strains. Most RDP types could be identified by a combination of serotype, infB allele, and inserted elements at each of the loci. These molecular markers can be used to identify GBS populations and to correlate RDP types and phylogenetic lineages identified by different methods.

Alleles↗