Comparative analysis of the localization and mobility of retrotransposons in sibling species Drosophila simulans and Drosophila melanogaster]

The distribution of four retrotransposon families (MDG1, MDG3, MDG4 and copia) on polytene chromosomes of different (from 9 to 15) Drosophila simulans strains is studied. The mean number of MDG1 and copia euchromatic hybridization sites (3 sites for each element) is drastically decreased in D. simulans in comparison with D. melanogaster (24 and 18 sites respectively). The mean number of MDG3 sites of hybridization is 5 in D. simulans against 12 in D. melanogaster. As for MDG4 both species have on the average about 2-3 euchromatic sites. The majority of MDG1 and copia and about a half of MDG3 euchromatic copies are localized in restricted number of sites (hot spots) on D. simulans polytene chromosomes. In D. melanogaster these elements are scattered along the chromosomes though there are some hot spots too. It appears that euchromatic copies of MDG1 and copia are considerably less mobile in D. simulans in contrast to D. melanogaster. Some common hot spots of retrotransposon localization in D. simulans and D. melanogaster were earlier described as intercalary heterochromatin regions in D. melanogaster. The level of interstrain variability of MDG4 hybridization sites is comparable in both species. Comparative blot-analysis of adult and larval salivary gland DNA shows that MDG1 and copia are situated mainly in euchromatic regions of D. melanogaster chromosomes. In D. simulans genome they are located mainly in heterochromatic regions underreplicated in salivary gland polytene chromosomes. There are interspecies differences in the distribution of retrotransposons in beta-heterochromatic chromosome regions.     

Expression of the quantitative trait radius incompletus in Drosophila and localization of mobile elements MDG1 and copia

A series of subpopulations earlier obtained were studied for hybridization of mobile genetic elements (MGE). The subpopulations examined were two "selected" (ris- and ris+), two "temperature" (ri(c113) and ri(c149)) and the control (ric). The method of in situ hybridization with polytene chromosomes of larval salivary glands was used to determine the patterns of MGE localization for all subpopulations. The patterns obtained appeared to be quite different from that of mdg-2. The trees of similarity for subpopulations according to the patterns of every MGE localization were built by conventional clustering methods. These trees were topologically similar to each other and to mdg-2. Distinction spectra of patterns of four daughter subpopulations, in comparison with the control one, were shown for each of these MGE to be independent and individual. However, there are some common regularities among copia-like MGE-mdg-1, copia, mdg-2 and, probably, mdg-3, namely: non-random property of the majority of changes, the similarity of patterns for subpopulations with similar phenotypes etc. So, Drosophila genome can be conceived as a complex system of patterns of different MGE localization, capable of common or independent mass transpositions after external stress action.     

Non-random distribution of spontaneous and high temperature-induced recessive lethal mutations in the X-chromosome of Drosophila]

Frequency and localization of spontaneous and induced by high temperature (37 degrees C) recessive lethal mutations in X-chromosome of females belonging to the 1(1) ts 403 strain defective in synthesis of heat-shock proteins (HSP) were studied. No differences in frequencies of both spontaneous and induced lethals between 1(1) ts 403 and control strain were found, thus implying that the disturbances in HSP synthesis have no effect on this process in oocytes of Drosophila melanogaster females. Surprisingly, distribution of spontaneous and induced lethals along the X-chromosome of 1(1) ts 403 strain appeared to be non-random: they primarily are located in its distal portion (1-44 cM of genetic map or in I-II sections of the Bridges cytogenetic map). This correlates with non-random distribution of mobile elements in the X-chromosome of D. melanogaster (Leibovich, 1990).     

Mobile genetic elements and quantitative characters in Drosophila: facts and hypotheses]

This review is dedicated to the comparison of the facts obtained and the proposed hypotheses, to the critical analysis of the situation arisen, and to the estimation of key propositions of the concept developed. The main point is that mobile genetic elements (MGEs) participate directly in expression, variability, selection and evolution of different quantitative characters. Genetic and selection data are considered, and hypotheses of random fixation, marker effect and direct participation of MGE patterns in expression and selection of quantitative characters are discussed. The consequences of temperature treatment are considered and hypotheses of masked selection and temperature induction of transpositions are discussed. The marker effects are shown to be non-sufficient to explain the properties of quantitative character radius incompletus system. The MGE patterns are important components of genetical system of determination of a quantitative character. MGEs modify, enhance the expression of neighbouring polygenes. Temperature effects could be explained by the influence of stress temperature treatment through the system of heat shock response on the capacity of MGEs to transcribe and transpose. The system of diversed MGE patterns in drosophila chromosomes could be believed to be universal genomic system of "soft" modification of the polygenic control of any limiting quantitative characters.     

Evolutionary significance of the presence in mobile genetic elements of regulatory sites reacting to the environment. Regulatory site as a trigger

A mathematical model of the Markov's process type describing the duplicative transposition of mobile genetic elements (MGE) has been developed. The possible role of MGE containing regulatory sites activated under unfavourable conditions has been considered. An analysis of the model has shown that there may be such regimes of environmental changes (sharp but random changes of the environment parameters) when sufficiently reliable survival of population is dependent on such MGE.     

Evolutionary, ecological and biotechnological perspectives on plasmids resident in the human gut mobile metagenome

Numerous mobile genetic elements (MGE) are associated with the human gut microbiota and collectively referred to as the gut mobile metagenome. The role of this flexible gene pool in development and functioning of the gut microbial community remains largely unexplored, yet recent evidence suggests that at least some MGE comprising this fraction of the gut microbiome reflect the co-evolution of host and microbe in the gastro-intestinal tract. In conjunction, the high level of novel gene content typical of MGE coupled with their predicted high diversity, suggests that the mobile metagenome constitutes an immense and largely unexplored gene-space likely to encode many novel activities with potential biotechnological or pharmaceutical value, as well as being important to the development and functioning of the gut microbiota. Of the various types of MGE that comprise the gut mobile metagenome, plasmids are of particular importance since these elements are often capable of autonomous transfer between disparate bacterial species, and are known to encode accessory functions that increase bacterial fitness in a given environment facilitating bacterial adaptation. In this article current knowledge regarding plasmids resident in the human gut mobile metagenome is reviewed, and available strategies to access and characterize this portion of the gut microbiome are described. The relative merits of these methods and their present as well as prospective impact on our understanding of the human gut microbiota is discussed.     

Transposition induction of the mobile genetic element Dm412 in the Drosophila genome using heat shock]

Males of Drosophila melanogaster isogenic line with oligogene mutation radius incompletus (ri) were exposed to standard heat-shock (SHS: t = 37 degrees C, 90 min) and heavy heat-shock (SHS: three-fold transfer of males from t = 37 degrees C, 2h, t0t = 4 degrees C 1 h, and back). At F1 of the treated males with untreated females of the same isogenic line mass transpositions of MGE Dm412 were found. The new positions of MGE seem to be not random, and 5 "hot sites" of transpositions were detected. The probabilities of transpositions were estimated after SHS and HHS and in control sample. They were, correspondingly, 3.4 x 10(-2), 8.7 x 10(-2) and less than 4.1 x 10(-4) transpositions per genome, per site occupied, per generation. Therefore, as a result of HS treatment, the probabilities of transpositions were two orders of magnitude increased as compared to control, directly at next generation after induction. Comparison of these results with those obtained after step-wise temperature treatment shows that induction is dependent rather of "stressor effect" of temperature treatment than of treatment way used.     

Molecular analysis of the rfaD gene, for heptose synthesis, and the rfaF gene, for heptose transfer, in lipopolysaccharide synthesis in Salmonella typhimurium.

We report the analysis of three open reading frames of Salmonella typhimurium LT2 which we identified as rfaF, the structural gene for ADP-heptose:LPS heptosyltransferase II; rfaD, the structural gene for ADP-L-glycero-D-manno-heptose-6-epimerase; and part of kbl, the structural gene for 2-amino-3-ketobutyrate CoA ligase. A plasmid carrying rfaF complements an rfaF mutant of S. typhimurium; rfaD and kbl are homologous to and in the same location as the equivalent genes in Escherichia coli K-12. The RfaF (heptosyl transferase II) protein shares regions of amino acid homology with RfaC (heptosyltransferase I), RfaQ (postulated to be heptosyltransferase III), and KdtA (ketodeoxyoctonate transferase), suggesting that these regions function in heptose binding. E. coli contains a block of DNA of about 1,200 bp between kbl and rfaD which is missing from S. typhimurium. This DNA includes yibB, which is an open reading frame of unknown function, and two promoters upstream of rfaD (P3, a heat-shock promoter, and P2). Both S. typhimurium and E. coli rfaD genes share a normal consensus promoter (P1). We postulate that the yibB segment is an insertion into the line leading to E. coli from the common ancestor of the two genera, though it could be a deletion from the line leading to S. typhimurium. The G+C content of the rfaLKZYJI genes of both S. typhimurium LT2 and E. coli K-12 is about 35%, much lower than the average of enteric bacteria; if this low G+C content is due to lateral transfer from a source of low G+C content, it must have occurred prior to evolutionary divergence of the two genera.     

The hand, foot and mouth disease virus capsid: sequence analysis and prediction of antigenic sites from homology modelling

Enterovirus 71 (EV71) is the most common aetiological agent detected in cases of hand, foot and mouth disease (HFMD) resulting in incidences of neurological complications and fatality in recent years. A comparison of the capsid proteins implicated in the pathogenicity of the fatal and non-fatal strains of EV71, reveals a high degree of homology (93%-100% identity). To facilitate diagnostic immunoassays and vaccine development, a consensus structural model for the EV71 coat protein has been developed based primarily on the homologous structure of the bovine enterovirus. The overall architecture of the virion closely resembles those of related icosahedral picornaviruses. Detailed atomic modelling of the fatal 5865/SIN/00009 strain has been carried out, and the functional regions (known and predicted) from closely related viruses mapped onto the surface of the predicted structure. From the model, we have identified two putative immunogenic regions, one of which is unique to EV71. The hydrophobic pocket within VP1, found in bovine enterovirus, poliovirus and rhinovirus, is also conserved in EV71.     

Integrated mobile genetic elements in Thaumarchaeota

To explore the diversity of mobile genetic elements (MGE) associated with archaea of the phylum Thaumarchaeota, we exploited the property of most MGE to integrate into the genomes of their hosts. Integrated MGE (iMGE) were identified in 20 thaumarchaeal genomes amounting to 2 Mbp of mobile thaumarchaeal DNA. These iMGE group into five major classes: (i) proviruses, (ii) casposons, (iii) insertion sequence-like transposons, (iv) integrative-conjugative elements and (v) cryptic integrated elements. The majority of the iMGE belong to the latter category and might represent novel families of viruses or plasmids. The identified proviruses are related to tailed viruses of the order Caudovirales and to tailless icosahedral viruses with the double jelly-roll capsid proteins. The thaumarchaeal iMGE are all connected within a gene sharing network, highlighting pervasive gene exchange between MGE occupying the same ecological niche. The thaumarchaeal mobilome carries multiple auxiliary metabolic genes, including multicopper oxidases and ammonia monooxygenase subunit C (AmoC), and stress response genes, such as those for universal stress response proteins (UspA). Thus, iMGE might make important contributions to the fitness and adaptation of their hosts. We identified several iMGE carrying type I-B CRISPR-Cas systems and spacers matching other thaumarchaeal iMGE, suggesting antagonistic interactions between coexisting MGE and symbiotic relationships with the ir archaeal hosts.     

Genomic instability in sunflower interspecific hybrids

The expression of genomic instability was studied at the phenotypical (morphological characters, electrophoretic spectra of seed storage proteins) and molecular (DNA amplification products) levels in interspecific hybrids (ISHs) from crosses of inbred lines of cultivated sunflower Helianthus annuus with perennial species of the genus Helianthus and in introgressive lines (ILs) produced on their basis. Unstable state of the locus determining the trait of lower branching was proved by the method of hybridological analysis. It was shown with the use of RAPD markers that the IL genome is characterized by instability even after long-term inbreeding (in generations F₈-F₁₂). In progenies of different combinations of interspecific crosses, identical polymorphic variants were revealed for a seed storage protein, helianthinin, and for DNA fragments homologous to structural genes of functionally important proteins, suggesting the nonrandom character of ISH genome variation. This variation may be determined by genome reorganizations under the action of a genome shock induced by interspecific hybridization. The factors inducing reorganizations in the genome include the activity of mobile genetic elements (MGEs). Using primers specific to different MGE families, nucleotide sequences with a high level of homology to the sequences of fragments of the mobile elements MuDR, Far1, CACTA, Stowaway, and Tourist were identified in the sunflower genome. The possibility of using MGE fragments for sunflower genotyping was demonstrated.     

The prevalence and diversity of mobile genetic elements in bacterial communities of different environmental habitats: insights gained from different methodological approaches

The pool of mobile genetic elements (MGE) in microbial communities consists of plasmids, bacteriophages and other elements that are either self-transmissible or use mobile plasmids and phages as vehicles for their dissemination. By facilitating horizontal gene exchange, the horizontal gene pool (HGP) promotes the evolution and adaptation of microbial communities. Efforts to characterise MGE from bacterial populations resident in a variety of ecological habitats have revealed a surprisingly vast and seemingly untapped diversity. MGE, conferring such selectable traits as mercury or antibiotic resistance and degradative functions, have been readily acquired from diverse microbial communities. To circumvent the need to isolate microbial hosts, polymerase chain reaction (PCR)-based detection methods have frequently been used to assess the prevalence of MGE-specific sequences resident in the ‘microbial community’ HGP. As studies continue to reveal novel and distinct MGE, sequencing of newly isolated MGE from diverse habitats is essential for the continued development of DNA probes, PCR primers as well as for gene array and proteomics-based approaches. This minireview highlights insight gained from different methodological approaches, biased albeit largely toward plasmids in Gram-negative bacteria, used to study the HGP of naturally occurring microbial communities from various aquatic and terrestrial habitats.     

Analysis of the primary structure of DNA sequences flanking MDG1

MDG is a very important component of the Drosophila genome. MDG have many sites of localisation in chromosomes and can change their localisation. Perhaps the process of MDG integration has some specificity. To study this problem we sequenced the flanking region of MDG1 DNA. The analysis of this sequences reveals the following features. 1. The 5'-flanking sequences contain 7 TATA-boxex, 5 of which form a cluster. 2. The 3'-flanking sequences contain TTTAAA block which is similar to TATA-box for alpha- and gamma-casein genes of mammals. 3. The flanking region are rich in repeated sequences, the longest of which TCCTCCT (R) and TTCTTC (R2) are on the 5'-flank and on the 3'-flank respectively, so that the whole structure is: 5'-R1NNR1-MDG1-R2NNR2-3', where N is some nucleotide. 5'-flanking sequences are AT-rich, while the 3'-flank contains 10 consecutive thymidines 4 nucleotides apart from MDG1. The MDG1 and MDG "17.6" share several common repeats in the flanking sequences, the longest of which TACTTACAT is 63 bases upstream MDG1 and 11 bases upstream MDG "17.6". This sequence differs strongly from the consensus enhancer sequence.