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Factors that Affect the Horizontal Transfer of Transposable Elements

Factors that Affect the Horizontal Transfer of Transposable Elements

Transposable elements are characterized by their ability to spread within a host genome. Many are also capable of crossing species boundaries to enter new genomes, a process known as horizontal transfer. Focusing mostly on animal transposable elements, we review the occurrence of horizontal transfer and examine the methods used to detect such transfers. We then discuss factors that affect the frequency of horizontal transfer, with emphasis on the mechanism and regulation of transposition. An intriguing feature of horizontal transfer is that its frequency differs among transposable element families. Evidence summarized in this review indicates that this pattern is due to fundamental differences between Class I and Class II elements. There appears to be a gradient in the incidence of horizontal transfer that reflects the presence of DNA intermediates during transposition. Furthermore, horizontal transfer seems to predominate among families for which copy number is controlled predominantly by self-regulatory mechanisms that limit transposition. We contend that these differences play a major role in the observed predominance of horizontal transfer among Class II transposable elements.
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Horizontal Transfer of Antibiotic Resistance Genes on Abiotic Touch Surfaces: Implications for Public Health

Horizontal Transfer of Antibiotic Resistance Genes on Abiotic Touch Surfaces: Implications for Public Health

Horizontal transfer of ␤-lactamase genes does not occur on antimicrobial copper surfaces. A reduction in the microbial bur- den and infection rate has previously been observed with dry cop- per alloy surfaces for other bacterial, viral, and fungal pathogens in laboratory studies and clinical trials incorporating copper alloys into a range of fitments, including door handles and push plates, toilet seats, bed rails, and intravenous poles in high-risk clinical and community environments throughout the world (18, 19, 22, 26–35). Previous work with enterococci has suggested that dry copper surfaces evoke death by release of copper ions and effects on growth and respiration; genomic and plasmid DNA is a pri- mary target (18, 22). DNA is also degraded in Gram-negative cells exposed to copper but not as rapidly; the cell membrane is a pri- mary target because depolarization occurs immediately on con- tact and peroxidation of membrane lipids occurs (32, 36). After we had observed HGT on stainless steel, we investigated whether it would occur on dry copper surfaces.
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Horizontal transfer of transposons between and within crustaceans and insects

Horizontal transfer of transposons between and within crustaceans and insects

Next we sought to assess the taxonomic distribution of Crmar2_Avul and Mariner-5_Avul in eukaryotes by per- forming BLASTn searches on all eukaryotic genomes that were available in Genbank as of May 2013. In addition to the species in which the two elements had previously been described (C. rosa, Anastrepha ludens and Anastrepha suspensa for Crmar2; D. biarmipes for Mariner-5_Dbi) we found TEs highly similar (>90% identity over >500 bp) to Crmar2_Avul in Drosophila ananassae and Drosophila bipectinata, and to Mariner- 5_Avul in the ant Harpegnathos saltator. Interestingly, the taxonomic distribution of the two elements is patchy, not only at the level of the arthropod phylogeny, but also within the lower level taxa in which we found them (Figure 1), a pattern likely indicative of horizontal transfer [17]. For example, Crmar2_Avul is only present in two closely related Drosophila species out of the 13 that we searched, and Mariner-5_Avul was identified only in one of the three hymenopteran genomes available.
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Evolution and Horizontal Transfer of dUTPase-Encoding Genes in Viruses and Their Hosts

Evolution and Horizontal Transfer of dUTPase-Encoding Genes in Viruses and Their Hosts

Mechanisms of horizontal transfer. Retroviruses may ac- quire sequences relatively easily from their hosts or from each other because of viral recombination or incorporation of host mRNA into the retroviral genome (23). A mature dut RNA message could theoretically be copackaged in a retrovirus and then incorporated into its genome. This might explain why none of the retroviral dut sequences have introns even though their vertebrate counterparts do; a pattern also observed in c- and v-oncogenes, for example c-myc (7). dUTPase is encoded in a different region in two different retrovirus lineages (MMTV relatives and nonprimate lentiviruses), despite its ab- sence in close relatives of these lineages. It is most reasonable to assume a horizontal transfer between the two lineages or independent acquisition of the gene, whereas a loss in all other relatives is highly unlikely. If convergence or parallelism were operating because both dUTPases function in a retroviral background, one might expect the generally conserved OSM to reflect this. It is the MIRs that support monophyly of the MMTV and nonprimate lentivirus dUTPases rather than the OSM (data not shown). In addition, a spuma-related retrovirus encodes a dUTPase in a third unique location (8). We have another study in progress to determine the relationship of this third type of retroviral dUTPase to the others. Due to the rapid rate of evolution in RNA genomes and consequent high sequence divergence, the source of these genes (host or retro- viral) may be undeterminable. It has recently been proposed that the outer domain of gp120 in primate lentivirus human immunodeficiency virus (HIV) also originated as a host dUTPase sequence (1). While it is possible that gp120 evolved from a dUTPase-like sequence, the extreme lack of conserved dUTPase residues between and within the dUTPase OSM in gp120 makes the identity of the original protein impossible to con- firm.
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Evolution of gene fusions: horizontal transfer versus independent events

Evolution of gene fusions: horizontal transfer versus independent events

In addition to their utility for functional prediction, analysis of gene fusions may help in addressing fundamental evolu- tionary issues. Gene fusions often show scattered phyletic patterns, appearing in several species from different lin- eages. By investigating the phylogenies of each of the two fusion-linked genes, it may be possible to determine the evo- lutionary scenario for the fusion itself. A recent study pro- vided evidence that the fission of fused genes occurred during evolution at a rate comparable to that of fusion [12]. Here, we address another central aspect of the evolution of gene fusions, namely, do fusions of the same domains in dif- ferent phylogenetic lineages reflect vertical descent, possibly accompanied by multiple lineage-specific fission events, or independent fusion events, or horizontal transfer of the fused gene? In other words, is a fusion of a given pair of genes extremely rare and, once formed, is it spread by hori- zontal gene transfer (HGT) perhaps also followed by fissions in some lineages? Alternatively, are independent fusions of the same gene pair in distinct lineages relatively common during evolution? Among fusions that are found in at least two of the three primary kingdoms of life (Bacteria, Archaea and Eukaryota), we detected both modes of evolution, but horizontal transfer of a fused gene appeared to be more common than independent fusion events or vertical inheri- tance with multiple fissions.
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Transposon Mediated Horizontal Transfer of the Host Specific Virulence Protein ToxA between Three Fungal Wheat Pathogens

Transposon Mediated Horizontal Transfer of the Host Specific Virulence Protein ToxA between Three Fungal Wheat Pathogens

a mosaic of repetitive coding regions. We propose that ToxhAT was transferred horizontally as, or by, a transposon, with the fitness advantage of ToxA fixing these HGT events in three wheat-infecting species. Similarly, the horizontally transferred regions in the cheese-making Penicillium spp. were flanked by unusual i non-LTR retrotransposons (13). In the present study, it remained unclear whether ectopic recombination, rather than active transposition, is the mechanism that integrates the HT DNA into the recipient genome. Horizontal transfer of transposons (HTT) has been widely reported in eukaryotes since the early discovery of P elements in Drosophila (66, 67). The literature on this topic, however, seems to clearly divide HGT from HTT as two separate phe- nomena, the latter being much more common (68–70). Recent reports of the HTT between insects has used noncoding regions flanking horizontally transferred genes to demonstrate that a viral parasite, with a broad insect host range, is the vector for the horizontally transferred DNA (71). This report highlights how insights from noncoding regions can bring these studies closer to a mechanistic understanding of the HGT event (71, 72). Other studies which report HGT of secondary metabolite clusters into and between fungal species often rely on phylogenetic methods performed using coding regions alone to detect these events (73–76). While these studies focus on the biolog- ical significance of the coding regions, clues to a possible mechanism may remain in the surrounding noncoding DNA.
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Horizontal transfer of a retrotransposon between parasitic nematodes and the common shrew

Horizontal transfer of a retrotransposon between parasitic nematodes and the common shrew

It is important to distinguish horizontal transfer from contamination of genetic material for example during sample collection. This is not a simple task but necessary if we are to understand if and how frequent horizontal transfers occur, and what the involved species are. Contamination has been previously erroneously identified as horizon- tal transfer in the literature [13]. The close physical and molecular association between a parasite and its host makes determining horizontal transfer a great challenge. We developed a new approach to distinguish between contamination and horizontal transfer that is similar in concept to existing methods. A common strategy to test for contamination is to examine flanking regions of trans- poson insertions [3]. If the flanking region does not origi- nate from the organism, the transposon is also considered as contamination. Another strategy is to compare the cov- erage of sequence reads at the transposon and in flanking regions [14]. To remove the factor of genome assembly issues that arise with repetitive regions, we devised a sim- ple strategy to directly determine contamination at the read level. In contrast to genome assemblies, read pairs and long reads are derived from a contiguous strand of DNA. Our approach takes reads that code for an RTE, and identifies the origin of the non-repetitive part of the read pairs or long reads (see Methods).
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Genetic exchange in eukaryotes through horizontal transfer: connected by the mobilome

Genetic exchange in eukaryotes through horizontal transfer: connected by the mobilome

As data is showing, wherever we compare genomes in any taxonomic level, one can find evidence of HTT (sections above) [96]. Large-scale studies (hundreds of insect species genomes) confirmed the previously suggested hypothesis [10] that close related taxa ex- change TEs by horizontal transfer more frequently than divergent ones [49]. Such findings have a major implica- tion on HTT pattern: most HTTs will continue to be found in close related species and we should expect fewer HTT cases in highly divergent species. However, evidence already exist for trans kingdom transfer of transposable elements: Lin et al. 2016 [19] described an ancient horizontal transfer (340Mya) of a Penelope retrotransposon from animals to plants (present in coni- fers but absent in other gymnosperms species) using an array of in silico and molecular techniques. More recently, Gao et al. 2017 [97] showed another evidence of HTT, now of a non-LTR retrotransposon, probably occurring between ancestral aphid or arthropod species to ancestral angiosperms.
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Horizontal transfer of aligned Si nanowire arrays and their photoconductive performance

Horizontal transfer of aligned Si nanowire arrays and their photoconductive performance

An easy and low-cost method to transfer large-scale horizontally aligned Si nanowires onto a substrate is reported. Si nanowires prepared by metal-assisted chemical etching were assembled and anchored to fabricate multiwire photoconductive devices with standard Si technology. Scanning electron microscopy images showed highly aligned and successfully anchored Si nanowires. Current-voltage tests showed an approximately twofold change in conductivity between the devices in dark and under laser irradiation. Fully reversible light switching ON/OFF response was also achieved with an I ON /I OFF ratio of 230. Dynamic response measurement showed a fast switching feature with response
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Horizontal transfer of BovB and L1 retrotransposons in eukaryotes

Horizontal transfer of BovB and L1 retrotransposons in eukaryotes

The placement of arthropods in the BovB tree is intri- guing, revealing potential HT vectors and the origin of BovB retrotransposons. For example, the RTE-like BovBs from butterflies, moths and ants appear as sister groups to the main BovB clade. This suggests that BovB TEs may have arisen as a subclass of ancient RTEs, countering the belief that they originated in squamates [14]. Within the central clade, we see a scattering of possible vector species including a leech (Helobdella robusta), two scorpion spe- cies (Mesobuthus martensii and Centruroides exilicauda) and a locust (Locusta migratoria). But the most interesting arthropod species is Cimex lectularius, the common bed bug, known to feed on animal blood. The full-length BovB sequence from Cimex shares > 80% identity to viper and cobra BovBs; their reverse transcriptase domains share > 90% identity at the amino acid level. Together, the bed bug and leech support the idea [8, 19] that blood-sucking parasites can transfer retrotransposons between the ani- mals they feed on.
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Horizontal Transfer of the Salmonella enterica Serovar Infantis Resistance and Virulence Plasmid pESI to the Gut Microbiota of Warm Blooded Hosts

Horizontal Transfer of the Salmonella enterica Serovar Infantis Resistance and Virulence Plasmid pESI to the Gut Microbiota of Warm Blooded Hosts

abundant conjugation opportunities. Thus, hosting the largest microbial community in the human body, the GI tract has been long suggested as “hot spot” for HGT between microbes (39–41). As a proof of this concept, we utilized the mouse infection model and demonstrated interspecies transfer of pESI from S. In- fantis to E. coli—members of the mouse gut microbiota. Further- more, different experimental approaches provided evidence for initial pESI transfer into Gram-positive microbiota as well. How- ever, whole-genome sequencing following two stages of subcul- turing in laboratory medium failed to detect pESI in the assembled genomes, suggesting that pESI cannot persist in these Gram- positive hosts. These results add to the previous few reports that were able to show conjugative transfer of a naturally occurring plasmid between Gram-negative and Gram-positive bacteria (42– 44). An interesting overrepresentation of pESI DNA was found particularly in Lactobacillus spp., possibly due to their hydrogen peroxide production (45, 46), shown here to further induce pilV transcription as well as pESI conjugation.
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Horizontal transfer and proliferation of Tsu4 in Saccharomyces paradoxus

Horizontal transfer and proliferation of Tsu4 in Saccharomyces paradoxus

Additional file 4 : Multiple sequence alignment of Ty4 and Tsu4 elements in Saccharomyces sensu stricto species.. Multiple sequence alignment of all full-length Ty4 / Tsu4 elements from [r]

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Horizontal transfer of a eukaryotic plastid-targeted protein gene to cyanobacteria

Horizontal transfer of a eukaryotic plastid-targeted protein gene to cyanobacteria

cifically involving the gene for its plastid-targeted FBA. However, such an event would lead to a simple distribu- tion of class I FBA in cyanobacteria where all taxa possess- ing the new gene were closely related to one another. This contrasts with the observed distribution shown in Figure 1, and is best exemplified by Prochlorococcus strains AS9601/MIT9301 and MIT9515/MED4, where apparently close relatives differ in the presence or absence of class I FBA. The complexity of this distribution suggests the evo- lution of class I FBA within Prochlorococcus and Synechococ- cus has been characterised either by further gene transfer events, or selective loss and retention of this eukaryotic gene across different strains. These two alternatives are described in greater detail below.
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Contribution of Horizontal Gene Transfer to the Evolution of Saccharomyces cerevisiae

Contribution of Horizontal Gene Transfer to the Evolution of Saccharomyces cerevisiae

variation of gene displacement. The ars-1 gene of N. crassa is a good example of the class of experimentally characterized aryl-sulfatase genes found in many fungi and animals, though not the Saccharomycetacea (12) or the “Saccharomyces com- plex” (29), which appears to have lost this eukaryotic aryl- sulfatase gene. Some species of hemiascomycetes, including C. albicans, D. hansenii, K. lactis, and Y. lipolytica, contain genes of a family related to ars-1. These sulfatase-like genes are of unknown function, however, and appear to be distantly related to the eukaryotic aryl-sulfatase genes (see Fig. S2 in the supplemental material). This sulfatase-like gene was also lost in the S. cerevisiae lineage after the divergence of the K. lactis and S. cerevisiae lineages. Neither the eukaryotic aryl-sulfatase gene nor the sulfatase-like gene appears in the genome of A. gossypii, C. glabrata, K. waltii, S. castellii, S. kluyveri, or any of the Saccharomyces sensu stricto species. The ars-1-encoded aryl-sulfatase of N. crassa is up-regulated by sulfur starvation and appears to function as a mechanism for sulfur scavenging (39). BDS1 shows higher expression in sulfur-limited chemo- stat cultures (4). It is possible that the acquisition of BDS1 was beneficial in that it restored aryl-sulfatase activity or was ben- eficial in that it provided the novel (for a eukaryote) activity of an alkyl-sulfatase. As is well known, horizontal gene transfer appears to be a mechanism for the acquisition of novel traits. Interestingly, however, horizontal transfer also appears to be a mechanism of genomic plasticity, allowing lineages to reac- quire traits and capabilities lost by their ancestors. Curiously, assuming that the established phylogeny of the Saccharomyces sensu stricto is correct, as BDS1 is found in S. cerevisiae and S. bayanus but does not appear in S. paradoxus and S. mikatae, it seems likely that this gene was lost in these species.
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Horizontal Gene Transfer of Functional Type VI Killing Genes by Natural Transformation

Horizontal Gene Transfer of Functional Type VI Killing Genes by Natural Transformation

As genomic analyses predict that transfer of entire T6SS operons frequently occurs in nature (16, 18), we tested this experimentally with toxigenic reference strain C6706, which is induced by chitin to become naturally transformable, and a nontransformable environmental isolate, 692-79 (12). At the Aux1 locus, both strains have distinct phospholipase effectors: TseL in C6706 and a phospholipase similar to Tle1 of Pseu- domonas aeruginosa in 692-79 (23, 24). The Aux2 operons of the two strains encode effectors with entirely different activities: a VasX pore-forming protein in C6706 and a LysM domain-containing effector that potentially targets peptidoglycan in 692-79 (25, 26). We recently demonstrated that the distinct T6 activities of these strains allowed them to engage in mutually antagonistic T6S killing (19). We therefore predicted that horizontal transfer of T6SS genes via natural transformation from a 692-79 donor to a C6706 recipient would generate transformants with T6SS profiles distinct from both donor and recipient strains. To test whether we could observe C6706 transformants that acquired the Aux alleles of the 692-79 donor, we introduced antibiotic resistance cassettes by recombination directly downstream of the Aux1 or Aux2 immunity genes in the 692-79 strain. To avoid challenges interpreting exchange of core and regulatory components, we did not design a system to measure exchange of large cluster components. When the two strains were cocultured on chitin tiles submerged in artificial seawater (ASW), C6706 acquired the entire Aux1 or Aux2 operon of 692-79 by natural transformation at frequencies of ~1 ⫻ 10 ⫺ 6 , while a nontransformable C6706
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Natural Competence Is a Major Mechanism for Horizontal DNA Transfer in the Oral Pathogen Porphyromonas gingivalis

Natural Competence Is a Major Mechanism for Horizontal DNA Transfer in the Oral Pathogen Porphyromonas gingivalis

ABSTRACT Porphyromonas gingivalis is a Gram-negative anaerobe that resides exclusively in the human oral cavity. Long-term colonization by P. gingivalis requires the bacteria to evade host immune responses while adapting to the changing host physiol- ogy and alterations in the composition of the oral microflora. The genetic diversity of P. gingivalis appears to reflect the variabil- ity of its habitat; however, little is known about the molecular mechanisms generating this diversity. Previously, our research group established that chromosomal DNA transfer occurs between P. gingivalis strains. In this study, we examine the role of putative DNA transfer genes in conjugation and transformation and demonstrate that natural competence mediated by comF is the dominant form of chromosomal DNA transfer, with transfer by a conjugation-like mechanism playing a minor role. Our results reveal that natural competence mechanisms are present in multiple strains of P. gingivalis, and DNA uptake is not sensi- tive to DNA source or modification status. Furthermore, extracellular DNA was observed for the first time in P. gingivalis bio- films and is predicted to be the major DNA source for horizontal transfer and allelic exchange between strains. We propose that exchange of DNA in plaque biofilms by a transformation-like process is of major ecological importance in the survival and per- sistence of P. gingivalis in the challenging oral environment.
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Experimental Study of Heat Transfer Coefficient of Water In Horizontal Tube

Experimental Study of Heat Transfer Coefficient of Water In Horizontal Tube

From the above results it is seen that with increase in the heat flux heat transfer rate is increasing with the quality content.The reason for this phenomenon is as the flow proceeds downstream and vaporization takes place, the void fraction is increases thus decreasing the density of the liquid vapor mixture. Result of this is flow is increases by enhancing convection transport from the heated wall of the tube. Results of the two is heat transfer coefficient at the point of transitions phase from nucleate boiling and convective is more.
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The advantages and disadvantages of horizontal gene transfer and the emergence of the first species

The advantages and disadvantages of horizontal gene transfer and the emergence of the first species

Thus I still think that if gene acquisition from diver- gent species is rare, then effective selection for barriers to transfer would not occur. To the contrary, the rare transfers that provide a selective advantage, and that are driven to fixation in the existing population, or that lead to the founding of a new population in a different niche conceivably could select for mechanism that enable HGT events between divergent organisms. Some of these HGTs have changed the face of this planet, e.g., the two photosystems working in series in oxygen pro- ducing photosynthesis [45,46], or the pathway that allows methane production from acetate in Methanosar- cina [47]. It is tempting to speculate that the creation of new metabolic pathways and capabilities was a driving force to select for and maintain HGT mechanism. While the idea of gene sharing mechanism providing an adaptive advantage is philosophically appealing to me, I do not know of any evidence that the transfer mechan- isms between divergent organisms are under purifying selection due to the selective advantage provided to the recipient (this is different for within group transfer, where the existence of Gene Transfer Agents whose sequences appear to be under purifying selection sug- gests selection for the gene transfer machinery [48]). Furthermore, the transfer of genes beneficial to the reci- pient (antibiotic or heavy metal resistance genes) often can be explained from the selfish gene point of view rather than assuming group selection in favour of HGT [49]. It appears possible that these transfer events, how- ever big their impact on the evolution of our biosphere, occurred as by products of other processes, such as uptake of DNA as a nutrient [27] as detailed by Vogan and Higgs, or as a by-product of the propagation of molecular parasites and viruses.
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Combined convection and other effects in heat transfer in horizontal flows

Combined convection and other effects in heat transfer in horizontal flows

In synthesis, the following has been treated: thermal inlet region with forced convection flow the standard Graetz problem, and with axial wall conduction the conjugate Graetz problem; b[r]

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Genomic insights into the rapid emergence and evolution of MDR in Staphylococcus pseudintermedius

Genomic insights into the rapid emergence and evolution of MDR in Staphylococcus pseudintermedius

Key works: Antimicrobial resistance, horizontal gene transfer, MRSP, whole genome.. 16.[r]

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