Types Of Genetic Elements Research Articles

Horizontal Gene Transfer, Fitness Costs and Mobility Shape the Spread of Antibiotic Resistance Genes into Experimental Populations of Acinetobacter Baylyi.

Horizontal gene transfer (HGT) is important for microbial evolution, but how evolutionary forces shape the frequencies of horizontally transferred genetic variants in the absence of strong selection remains an open question. In this study, we evolve laboratory populations of Acinetobacter baylyi (ADP1) with HGT from two clinically relevant strains of multidrug-resistant Acinetobacter baumannii (AB5075 and A9844). We find that DNA can cross the species barrier, even without strong selection, and despite substantial DNA sequence divergence between the two species. Our results confirm previous findings that HGT can drive the spread of antibiotic resistance genes (ARGs) without selection for that antibiotic, but not for all of the resistance genes present in the donor genome. We quantify the costs and benefits of horizontally transferred variants and use whole population sequencing to track the spread of ARGs from HGT donors into antibiotic-sensitive recipients. We find that even though most ARGs are taken up by populations of A. baylyi, the long-term fate of an individual gene depends both on its fitness cost and on the type of genetic element that carries the gene. Interestingly, we also found that an integron, but not its host plasmid, is able to spread in A. baylyi populations despite its strong deleterious effect. Altogether, our results show how HGT provides an evolutionary advantage to evolving populations by facilitating the spread of non-selected genetic variation including costly ARGs.

Non-coding RNAs in GI cancers: from cancer hallmarks to clinical utility

One of the most unexpected discoveries in molecular oncology, in the last decades, was the identification of a new layer of protein coding gene regulation by transcripts that do not...

Mind the gap; seven reasons to close fragmented genome assemblies

Like other domains of life, research into the biology of filamentous microbes has greatly benefited from the advent of whole-genome sequencing. Next-generation sequencing (NGS) technologies have revolutionized sequencing, making genomic sciences accessible to many academic laboratories including those that study non-model organisms. Thus, hundreds of fungal genomes have been sequenced and are publically available today, although these initiatives have typically yielded considerably fragmented genome assemblies that often lack large contiguous genomic regions. Many important genomic features are contained in intergenic DNA that is often missing in current genome assemblies, and recent studies underscore the significance of non-coding regions and repetitive elements for the life style, adaptability and evolution of many organisms. The study of particular types of genetic elements, such as telomeres, centromeres, repetitive elements, effectors, and clusters of co-regulated genes, but also of phenomena such as structural rearrangements, genome compartmentalization and epigenetics, greatly benefits from having a contiguous and high-quality, preferably even complete and gapless, genome assembly. Here we discuss a number of important reasons to produce gapless, finished, genome assemblies to help answer important biological questions.

How to deal with the upcoming challenges in GMO detection in food and feed.

Biotech crops are the fastest adopted crop technology in the history of modern agriculture. The commercialisation of GMO is in many countries strictly regulated laying down the need for traceability and labelling. To comply with these legislations, detection methods are needed. To date, GM events have been developed by the introduction of a transgenic insert (i.e., promoter, coding sequence, terminator) into the plant genome and real-time PCR is the detection method of choice. However, new types of genetic elements will be used to construct new GMO and new crops will be transformed. Additionally, the presence of unauthorised GMO in food and feed samples might increase in the near future. To enable enforcement laboratories to continue detecting all GM events and to obtain an idea of the possible presence of unauthorised GMO in a food and feed sample, an intensive screening will become necessary. A pragmatic, cost-effective, and time-saving approach is presented here together with an overview of the evolution of the GMO and the upcoming needs.

Comparative genomics reveal the mechanism of the parallel evolution of O157 and non-O157 enterohemorrhagic Escherichia coli

Among the various pathogenic Escherichia coli strains, enterohemorrhagic E. coli (EHEC) is the most devastating. Although serotype O157:H7 strains are the most prevalent, strains of different serotypes also possess similar pathogenic potential. Here, we present the results of a genomic comparison between EHECs of serotype O157, O26, O111, and O103, as well as 21 other, fully sequenced E. coli/Shigella strains. All EHECs have much larger genomes (5.5-5.9 Mb) than the other strains and contain surprisingly large numbers of prophages and integrative elements (IEs). The gene contents of the 4 EHECs do not follow the phylogenetic relationships of the strains, and they share virulence genes for Shiga toxins and many other factors. We found many lambdoid phages, IEs, and virulence plasmids that carry the same or similar virulence genes but have distinct evolutionary histories, indicating that independent acquisition of these mobile genetic elements has driven the evolution of each EHEC. Particularly interesting is the evolution of the type III secretion system (T3SS). We found that the T3SS of EHECs is composed of genes that were introduced by 3 different types of genetic elements: an IE referred to as the locus of enterocyte effacement, which encodes a central part of the T3SS; SpLE3-like IEs; and lambdoid phages carrying numerous T3SS effector genes and other T3SS-related genes. Our data demonstrate how E. coli strains of different phylogenies can independently evolve into EHECs, providing unique insights into the mechanisms underlying the parallel evolution of complex virulence systems in bacteria.

Evolution of mutational robustness in the yeast genome: a link to essential genes and meiotic recombination hotspots.

Deleterious mutations inevitably emerge in any evolutionary process and are speculated to decisively influence the structure of the genome. Meiosis, which is thought to play a major role in handling mutations on the population level, recombines chromosomes via non-randomly distributed hot spots for meiotic recombination. In many genomes, various types of genetic elements are distributed in patterns that are currently not well understood. In particular, important (essential) genes are arranged in clusters, which often cannot be explained by a functional relationship of the involved genes. Here we show by computer simulation that essential gene (EG) clustering provides a fitness benefit in handling deleterious mutations in sexual populations with variable levels of inbreeding and outbreeding. We find that recessive lethal mutations enforce a selective pressure towards clustered genome architectures. Our simulations correctly predict (i) the evolution of non-random distributions of meiotic crossovers, (ii) the genome-wide anti-correlation of meiotic crossovers and EG clustering, (iii) the evolution of EG enrichment in pericentromeric regions and (iv) the associated absence of meiotic crossovers (cold centromeres). Our results furthermore predict optimal crossover rates for yeast chromosomes, which match the experimentally determined rates. Using a Saccharomyces cerevisiae conditional mutator strain, we show that haploid lethal phenotypes result predominantly from mutation of single loci and generally do not impair mating, which leads to an accumulation of mutational load following meiosis and mating. We hypothesize that purging of deleterious mutations in essential genes constitutes an important factor driving meiotic crossover. Therefore, the increased robustness of populations to deleterious mutations, which arises from clustered genome architectures, may provide a significant selective force shaping crossover distribution. Our analysis reveals a new aspect of the evolution of genome architectures that complements insights about molecular constraints, such as the interference of pericentromeric crossovers with chromosome segregation.

Reticulate Representation of Evolutionary and Functional Relationships between Phage Genomes

Bacteriophage genomes show pervasive mosaicism, indicating the importance of horizontal gene exchange in their evolution. Phage genomes represent unique combinations of modules, each of them with a different phylogenetic history. The traditional classification, based on a variety of criteria such as nucleic acid type (single/double-stranded DNA/RNA), morphology, and host range, appeared inconsistent with sequence analyses. With the genomic era, an ever increasing number of sequenced phages cannot be classified, in part due to a lack of morphological information and in part to the intrinsic incapability of tree-based methods to efficiently deal with mosaicism. This problem led some virologists to call for a moratorium on the creation of additional taxa in the order Caudovirales, in order to let virologists discuss classification schemes that might better suit phage evolution. In this context, we propose a framework for a reticulate classification of phages based on gene content. Starting from gene families, we built a weighted graph, where nodes represent phages and edges represent phage-phage similarities in terms of shared genes. We then apply various measures of graph topology to analyze the resulting graph. Most double-stranded DNA phages are found in a single component. The values of the clustering coefficient and closeness distinguish temperate from virulent phages, whereas chimeric phages are characterized by a high betweenness coefficient. We apply a 2-step clustering method to this graph to generate a reticulate classification of phages: Each phage is associated with a membership vector, which quantitatively characterizes its membership to the set of clusters. Furthermore, we cluster genes based on their "phylogenetic profiles" to define "evolutionary cohesive modules." In virulent phages, evolutionary modules span several functional categories, whereas in temperate phages they correspond better to functional modules. Moreover, despite the fact that modules only cover a fraction of all phage genes, phage groups can be distinguished by their different combination of modules, serving the bases for a higher level reticulate classification. These 2 classification schemes provide an automatic and dynamic way of representing the relationships within the phage population and can be extended to include newly sequenced phage genomes, as well as other types of genetic elements.

Multiple Genetic Elements Carry the Tetracycline Resistance Gene tet (W) in the Animal Pathogen Arcanobacterium pyogenes

The tet(W) gene is associated with tetracycline resistance in a wide range of bacterial species, including obligately anaerobic rumen bacteria and isolates from the human gut and oral mucosa. However, little is known about how this gene is disseminated and the types of genetic elements it is carried on. We examined tetracycline-resistant isolates of the animal commensal and opportunistic pathogen Arcanobacterium pyogenes, all of which carried tet(W), and identified three genetic elements designated ATE-1, ATE-2, and ATE-3. These elements were found in 25%, 35%, and 60% of tetracycline-resistant isolates, respectively, with some strains carrying both ATE-2 and ATE-3. ATE-1 shows characteristics of a mobilizable transposon, and the tet(W) genes from strains carrying this element can be transferred at low frequencies between A. pyogenes strains. ATE-2 has characteristics of a simple transposon, carrying only the resistance gene and a transposase, while in ATE-3, the tet(W) gene is associated with a streptomycin resistance gene that is 100% identical at the DNA level with the aadE gene from the Campylobacter jejuni plasmid pCG8245. Both ATE-2 and ATE-3 show evidence of being carried on larger genetic elements, but conjugation to other strains was not observed under the conditions tested. ATE-1 was preferentially associated with A. pyogenes strains of bovine origin, while ATE-2 and ATE-3 elements were primarily found in porcine isolates, suggesting that these elements may circulate in different environments. In addition, four alleles of the tet(W) gene, primarily associated with different elements, were detected among A. pyogenes isolates.

Meiotic drive at the Om locus in wild-derived inbred mouse strains

Meiotic drive is an evolutionary force in which natural selection is uncoupled from organismal fitness. Recently, it has been proposed that meiotic drive and genetic drift represent major forces in the evolution of the mammalian karyotype. Meiotic drive involves two types of genetic elements, Responders and Distorters, the latter being required to induce transmission ratio distortion at the former. We have previously described the Om meiotic drive system in mouse chromosome 11. To investigate the natural history of this drive system we have characterized the alleles present at the distorter in wild-derived inbred strains. Our analysis of transmission of maternal alleles in both classical and wild-derived inbred strains indicated that driving alleles are found at high frequency in natural populations and that the existence of driving alleles predates the split between the Mus spicilegus and M. musculus lineages.

Impact of pathogenicity islands in bacterial diagnostics

Pathogenicity islands (PAIs) are a distinct class of genomic islands (GEIs), which are acquired by horizontal gene transfer. PAIs harbour virulence genes and some, in addition, antibiotic resistance genes. More often genes conferring antibiotic resistance are encoded by GEIs not containing virulence genes. Both types of genetic elements are found in genomes of various human, animal and plant pathogens. There are PAIs and GEIs which are specific for a certain serotype(s), strain, or pathotype of a species. Furthermore, there are also PAIs which are more widespread and found in bacterial pathogens causing a certain pathogenic effect in the host. Even the lack of a certain PAI might be characteristic for a defined subspecies. Obviously, PAIs can be used as markers for diagnostic purposes to help identify a certain bacterial pathogen, subtype it, estimate the pathogenic potential, and in some cases predict its antibiotic resistance. This all might be achieved for known PAIs/GEIs without cultivating the microorganism of interest by employing PCR and/or DNA-chip technology. Even yet unknown PAIs can be identified in silico if the genome sequence of the bacterial pathogen under investigation is known. The more PAIs and antibiotic harbouring GEIs are identified and characterized the greater will be the benefits also for diagnostics.

The [KIL-d] element specifically regulates viral gene expression in yeast.

The cytoplasmically inherited [KIL-d] element epigenetically regulates killer virus gene expression in Saccharomyces cerevisiae. [KIL-d] results in variegated defects in expression of the M double-stranded RNA viral segment in haploid cells that are "healed" in diploids. We report that the [KIL-d] element is spontaneously lost with a frequency of 10(-4)-10(-5) and reappears with variegated phenotypic expression with a frequency of > or =10(-3). This high rate of loss and higher rate of reappearance is unlike any known nucleic acid replicon but resembles the behavior of yeast prions. However, [KIL-d] is distinct from the known yeast prions in its relative guanidinium hydrochloride incurability and independence of Hsp104 protein for its maintenance. Despite its transmissibility by successive cytoplasmic transfers, multiple cytoplasmic nucleic acids have been proven not to carry the [KIL-d] trait. [KIL-d] epigenetically regulates the expression of the M double-stranded RNA satellite virus genome, but fails to alter the expression of M cDNA. This specificity remained even after a cycle of mating and meiosis. Due to its unique genetic properties and viral RNA specificity, [KIL-d] represents a new type of genetic element that interacts with a viral RNA genome.

Herpes simplex virus type 1-based amplicon vector systems

Publisher Summary This chapter discusses the development of the herpes simplex virus type 1 (HSV-1) amplicon as an efficient gene transfer vehicle, with emphasis on recent advances that have reduced toxic effects associated with the vector and increased both the efficiency of gene transfer and the stability of gene expression. HSV-1-based amplicon vectors have a great potential for applications in gene therapy, because they have a large transgene capacity and can efficiently transduce most cell types, both dividing and nondividing. The HSV-1 amplicon contains three types of genetic elements—namely, (1) sequences that allow its propagation as a bacterial plasmid, (2) a transgene cassette with the genes of interest, and (3) ∼1% of the 152-kb HSV-1 genome, in particular an origin of DNA replication and a DNA cleavage/packaging signal. These two noncoding, cis-acting HSV-1 elements are sufficient for supporting the replication of amplicon DNA and subsequent packaging into HSV-1 virions in the presence of helper functions. HSV-1, a member of the subfamily Alphaherpesvirinae , is a common pathogen in humans and one of the most extensively characterized viruses. The lytic cycle of the HSV-1 infection usually causes only mild symptoms, such as cold sores, and is rapidly controlled by the immune system.

Effects of Intraspecific Variation on Phylogenetic Inference: A Likelihood Analysis of mtDNA Restriction Site Data in Cyprinid Fishes

The comparative analysis of DNA molecules is a useful means for phylogenetic reconstruction, because different types of genetic elements yield resolution at different levels of taxonomic divergence. A single individual is usually characterized for each operational taxonomic unit (OTU), based on the premise that within-OTU variation can be safely ignored. Whereas that premise is expedient, it may not be generally valid. Sometimes variation within OTUs can affect the analysis. We develop a formal analytic treatment of variation in phylogenetic output as a consequence of intraspecific variation. Using restriction site data from the mitochondria of three species of cyprinid fishes to illustrate, we show that genetic variation within taxa impacts on tree topology

Group II twintron: an intron within an intron in a chloroplast cytochrome b-559 gene.

The psbF gene of chloroplast DNAs encodes the beta-subunit of cytochrome b-559 of the photosystem II reaction center. The psbF locus of Euglena gracilis chloroplast DNA has an unusual 1042 nt group II intron that appears to be formed from the insertion of one group II intron into structural domain V of a second group II intron. Using both direct primer extension cDNA sequencing and cDNA cloning and sequencing, we have determined that a 618 nt internal intron is first excised from the 1042 nt intron of psbF pre-mRNA, resulting in a partially spliced pre-mRNA containing a 424 nt group II intron with a spliced domain V. The 424 nt intron is then removed to yield the mature psbF mRNA. Therefore, the 1042 nt intron of psbF is a group II intron within another group II intron. We use the term 'twintron' to define this new type of genetic element. Intermediates in the splicing pathway were detected by northern hybridization. Splicing of both the internal and external introns occurs via lariat intermediates. Twintron splicing was found to proceed by a sequential pathway, the internal intron being removed prior to the excision of the external intron. A possible mechanism for twintron formation by intron transposition is discussed.

Integration of foreign DNA following microinjection of tobacco mesophyll protoplasts

DNA from a bacterial plasmid containing the T-DNA border sequences of Agrobacterium tumefaciens was transferred into the nucleus or the cytoplasm of tobacco mesophyll protoplasts by microinjection. Following culture in hanging drops, some of these protoplasts produced calli containing the foreign DNA sequences. Evidence for the presence of the injected plasmid DNA in these calli was provided by Southern hybridization analysis. The results demonstrated that random portions of the bacterial plasmid were linked to plant DNA and that integration did not occur at the T-DNA borders present on the injected plasmid. The average number of integrated copies ranged from less than one to 1–2 per tobacco genome. The frequency of integration averaged 14% with intranuclear injections compared to 6% with cytoplasmic injections. With further refinement, the use of microinjection may allow the introduction of many different types of genetic elements into plants.

Terminal direct repeats in a retrovirus-like repeated mouse gene family

The mouse genome contains multiple copies of a dispersed gene family known individually as VL30 genes which are thought to be associated with retroviruses. The copies consist of closely related 5.2-kilobase DNA sequences flanked by unrelated cellular DNA, and although no sequence homology has been found between the genes and the exogenous or endogenous retroviruses so far tested, the 30S RNA transcripts expressed by the genes are efficiently packaged into virions, recovered from infected cells and transmitted to other cells by pseudo-type infection. Stimulated by recent reports of the similarity between retroviruses and transposons (from which retroviruses may have evolved), and in particular by the recognition that both types of genetic elements are characterized by a large terminal repeat (LTR), we set out to determine whether the VL30 genes are also distinguished by this property. Using cloned DNAs from a mouse gene library and heteroduplex analysis, we have now found that the VL30 genes do indeed carry terminal direct repeats 400 base pairs long.

IS-elements in bacteria.

The first extrachromosomal genetic elements discovered in bacteria were temperate bacteriophages, which can exist either as extracellular virus, as chromosomes replicating autonomously within cells or integrated into the bacterial chromosome. Integration of viruses into host chromosomes has subsequently attracted considerable attention by tumor virologists. This may justify the discussion of other types of genetic elements in bacteria in a meeting on human leucaemia.