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.     

Mobile elements and mammalian genome evolution

Mobile elements make up large portions of most eukaryotic genomes. They create genetic instability, not only through insertional mutation but also by contributing recombination substrates, both during and long after their insertion. The combination of whole-genome sequences and the development of innovative new assays to test the function of mobile elements have increased our understanding of how these elements mobilize and how their insertion impacts genome diversity and human disease.     

Mobile genetic elements and sexual reproduction

Transposable elements (TE) are prominent components of most eukaryotic genomes. In addition to their possible participation in the origin of sexual reproduction in eukaryotes, they may be also involved in its maintenance as important contributors to the deleterious mutation load. Comparative analyses of transposon content in the genomes of sexually reproducing and anciently asexual species may help to understand the contribution of different TE classes to the deleterious load. The apparent absence of deleterious retrotransposons from the genomes of ancient asexuals is in agreement with the hypothesis that they may play a special role in the maintenance of sexual reproduction and in early extinction for which most species are destined upon the abandonment of sex.     

Concerted evolution between duplicated genetic elements in Helicobacter pylori

The Helicobacter pylori genome includes a family of outer membrane proteins (OMPs) with substantial N and C-terminal identity. To better understand their evolution, the nucleotide sequences for two members, babA and babB, were determined from a worldwide group of 23 strains. The geographic origin of each strain was found to be the major determinant of phylogenetic structure, with strains of Eastern and Western origin showing greatest divergence. For strains 96-10 (Japan) and 96-74 (USA), the 5' regions of babB are replaced with babA sequences, demonstrating that recombination occurs between the two loci. babA and babB have nearly equivalent variation in nucleotide and amino acid identity, and frequencies of synonymous and non-synonymous substitutions. Both genes have segmental conservation but within the 3' segment, substitution patterns are nearly identical. Although babA and babB 5' and midregion segment phylogenies show strong interstrain similarity, the 3' segments show strong intrastrain similarity, indicative of concerted evolution. Within these 3' segments, the lower intrastrain than interstrain frequencies of nucleotide substitutions, which are below mean background H. pylori substitution frequencies, indicate selection against intrastrain diversification. Since babA/babB gene conversions likely underlie the concerted evolution of the 3' segments, in an experimental system, we demonstrate that gene conversions can frequently (10(-3)) occur in H. pylori. That these events are recA-dependent and DNase-resistant indicates their likely cause is intragenomic recombination.     

Sexual dimorphism and the genetic potential for evolution of sex allocation in the gynodioecious plant, Schiedea salicaria

Sex allocation theory addresses how separate sexes can evolve from hermaphroditism but little is known about the genetic potential for shifts in sex allocation in flowering plants. We tested assumptions of this theory using the common currency of biomass and measurements of narrow-sense heritabilities and genetic correlations in Schiedea salicaria, a gynodioecious species under selection for greater differentiation of the sexes. Female (carpel) biomass showed heritable variation in both sexes. Male (stamen) biomass in hermaphrodites also had significant heritability, suggesting the potential for further evolution of dioecy. Significant positive genetic correlations between females and hermaphrodites in carpel mass may slow differentiation between the sexes. Within hermaphrodites, there were no negative genetic correlations between male and female biomass as assumed by models for the evolution of dioecy, suggesting that S. salicaria is capable of further changes in biomass allocation to male and female functions and evolution toward dioecy.     

Mobile dispersed genetic elements and their possible relation to carcinogenesis

In this paper, a hypothesis is described according to which mobile dispersed genetic elements are related to endogenous viral genomes and may be involved in oncogenic transformation by uptaking cellular genes important for cellular growth. It is also possible that, in certain cases, they can switch off the genes involved in the control of differentiation.     

Applying mobile genetic elements for genome analysis and evolution

Transposable elements (TEs) are ubiquitous components of all living organisms, and in the course of their coexistence with their respective host geneomes, these parasitc DNAs have played important roles in the evolution of complex genetic networks. The interaction between mobile DNAs and their host genomes are quite diverse, ranging from modifications of gene structure and regulation to alterations in general genome architecture. Thus during evolutionary time these elements can be regarded as natural molecular tools in shaping the organization, structure, and function of eukaryotic genes and genomes. Based on their intrinsic properties and features, mobile DNAs are widely applied at present as a technical “toolbox”, essential for studying a diverse spectrum of biological questions. In this review, we aim to summarize both the evolutionary impact of TEs on geneome evolution and their valuable and diverse methodological applications as molecular tools.     

Mobile dispersed genetic elements in eukaryotes and their possible relationship to carcinogenesis

During last three years, the mobile dispersed genetic elements (mdg) were isolated from the genome of Drosophila melanogaster, yeasts and mammals. According to a number of their properties, mdg elements are quite similar to endogenous pro-retroviruses. It is known that in many cases oncogeneity of retroviruses depends on the incorporation of the certain host genes (potential oncogenes) into the viral genome. We suggest that in some cases mdg elements could entrap the potential oncogenes in the course of transposition. As a result, oncogenes become uncontrollable by host regulatory systems and may induce cell transformation. Another possible mechanism underlying switch off of the gene responsible for differentiation control may be mdg transposition to a region in close vicinity of the gene. As transposition of mdg elements seems to occur rather often, they may be regarded as one of the most important factors of genome rearrangements leading to cell transformation.     

Transposable element-medicated evolution of sex: A population genetic model

For a population made up of individuals capable of sexual as well as asexual modes of reproduction, conditions for the spread of a transposable element are explored using a one-locus, two-haplotype model. The analysis is then extended to include the possibility that the transposable element can modulate the probability of sexual reproduction, thus casting Hickey’s (1982,Genetics 101: 519–531) suggestion in a population genetics framework. The model explicitly includes the cost of sexual reproduction, fitness disadvantage to the transposable element, probability of transposition, and the predisposition for sexual reproduction in the presence and absence of the transposable element. The model predicts several kinds of outcome, including initial frequency dependence and stable polymorphism. More importantly, it is seen that for a wide range of parameter values, the transposable element can go to fixation. Therefore it is able to convert the population from a predominantly asexual to a predominantly sexual mode of reproduction. Viewed in conjunction with recent results implicating short stretches of apparently non-coding DNA in sex determination (McCoubreyet al. 1988,Science 242: 1146–1151), the model hints at the important role this mechanism could have played in the evolution of sexuality.     

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.     

The evolution of cultivated plant species: classical plant breeding versus genetic engineering

Agriculture is the most intensive form of environmental exploitation performed by mankind. It involves replacing the natural ecosystem with an artificial plant community comprising one or more crop species, and weeds can invade the cleared land. Initially, the adoption of agriculture did not necessarily imply an improvement in standard of living (there is, in fact, evidence to the contrary), but as agricultural efficiency improved, surpluses were generated on top of mere subsistence levels. It may take many years of labor in order to obtain a crop that has all of the desired traits. It is not possible to control which genes are transferred from the parents to the offspring, and the results are often uncertain. In comparison, the utilization of genetic engineering to improve crops can be a faster and more precise approach. Unlike traditional breeding, genetic engineering makes it possible to select the specific traits desired and insert the genes that code for them into the plant.     

Mobile genetic elements in the genome of the beneficial rhizobacterium Pseudomonas fluorescens Pf-5

Background

Three percent of the world's population is chronically infected with hepatitis C virus (HCV) and thus at risk of developing liver cancer. Although precise mechanisms regulating HCV entry into hepatic cells are still unknown, several cell surface proteins have been identified as entry factors for this virus. Among these molecules, the tetraspanin CD81 is essential for HCV entry. Interestingly, CD81 is also required for Plasmodium infection. A major characteristic of tetraspanins is their ability to interact with each other and other transmembrane proteins to build tetraspanin-enriched microdomains (TEM).

Results

In our study, we describe a human hepatoma Huh-7 cell clone (Huh-7w7) which has lost CD81 expression and can be infected by HCV when human CD81 (hCD81) or mouse CD81 (mCD81) is ectopically expressed. We took advantage of these permissive cells expressing mCD81 and the previously described MT81/MT81w mAbs to analyze the role of TEM-associated CD81 in HCV infection. Importantly, MT81w antibody, which only recognizes TEM-associated mCD81, did not strongly affect HCV infection. Furthermore, cholesterol depletion, which inhibits HCV infection and reduces total cell surface expression of CD81, did not affect TEM-associated CD81 levels. In addition, sphingomyelinase treatment, which also reduces HCV infection and cell surface expression of total CD81, raised TEM-associated CD81 levels.

Conclusion

In contrast to Plasmodium infection, our data show that association of CD81 with TEM is not essential for the early steps of HCV life cycle, indicating that these two pathogens, while using the same molecules, invade their host by different mechanisms.