Horizontal gene transfer

Horizontal gene transfer (HGT) or lateral gene transfer (LGT)[1][2][3] is the movement of genetic material between unicellular and/or multicellular organisms other than by the ("vertical") transmission of DNA from parent to offspring (reproduction).[4] HGT is an important factor in the evolution of many organisms.[5][6]

Horizontal gene transfer is the primary mechanism for the spread of antibiotic resistance in bacteria,[5][7][8][9][10] and plays an important role in the evolution of bacteria that can degrade novel compounds such as human-created pesticides[11] and in the evolution, maintenance, and transmission of virulence.[12] It often involves temperate bacteriophages and plasmids.[13][14][15] Genes responsible for antibiotic resistance in one species of bacteria can be transferred to another species of bacteria through various mechanisms of HGT such as transformation, transduction and conjugation, subsequently arming the antibiotic resistant genes' recipient against antibiotics. The rapid spread of antibiotic resistance genes in this manner is becoming medically challenging to deal with. Ecological factors may also play a role in the LGT of antibiotic resistant genes.[16] It is also postulated that HGT promotes the maintenance of a universal life biochemistry and, subsequently, the universality of the genetic code.[17]

Most thinking in genetics has focused upon vertical transfer, but the importance of horizontal gene transfer among single-cell organisms is beginning to be acknowledged.[18][19]

Gene delivery can be seen as an artificial horizontal gene transfer, and is a form of genetic engineering.

Tree Of Life (with horizontal gene transfer)
Tree of life showing vertical and horizontal gene transfers

History

Griffith's experiment, reported in 1928 by Frederick Griffith,[20] was the first experiment suggesting that bacteria are capable of transferring genetic information through a process known as transformation.[21][22] Griffith's findings were followed by research in the late 1930s and early 40s that isolated DNA as the material that communicated this genetic information.

Horizontal genetic transfer was then described in Seattle in 1951, in a paper demonstrating that the transfer of a viral gene into Corynebacterium diphtheriae created a virulent strain from a non-virulent strain,[23] also simultaneously solving the riddle of diphtheria (that patients could be infected with the bacteria but not have any symptoms, and then suddenly convert later or never),[24] and giving the first example for the relevance of the lysogenic cycle.[25] Inter-bacterial gene transfer was first described in Japan in a 1959 publication that demonstrated the transfer of antibiotic resistance between different species of bacteria.[26][27] In the mid-1980s, Syvanen[28] predicted that lateral gene transfer existed, had biological significance, and was involved in shaping evolutionary history from the beginning of life on Earth.

As Jian, Rivera and Lake (1999) put it: "Increasingly, studies of genes and genomes are indicating that considerable horizontal transfer has occurred between prokaryotes"[29] (see also Lake and Rivera, 2007).[30] The phenomenon appears to have had some significance for unicellular eukaryotes as well. As Bapteste et al. (2005) observe, "additional evidence suggests that gene transfer might also be an important evolutionary mechanism in protist evolution."[31]

Grafting of one plant to another can transfer chloroplasts (organelles in plant cells that conduct photosynthesis), mitochondrial DNA, and the entire cell nucleus containing the genome to potentially make a new species.[32] Some Lepidoptera (e.g. monarch butterflies and silkworms) have been genetically modified by horizontal gene transfer from the wasp bracovirus.[33] Bites from the insect Reduviidae (assassin bug) can, via a parasite, infect humans with the trypanosomal Chagas disease, which can insert its DNA into the human genome.[34] It has been suggested that lateral gene transfer to humans from bacteria may play a role in cancer.[35]

Aaron Richardson and Jeffrey D. Palmer state: "Horizontal gene transfer (HGT) has played a major role in bacterial evolution and is fairly common in certain unicellular eukaryotes. However, the prevalence and importance of HGT in the evolution of multicellular eukaryotes remain unclear."[36]

Due to the increasing amount of evidence suggesting the importance of these phenomena for evolution (see below) molecular biologists such as Peter Gogarten have described horizontal gene transfer as "A New Paradigm for Biology".[37]

Mechanisms

There are several mechanisms for horizontal gene transfer:[5][38][39]

Horizontal transposon transfer

A transposable element (TE) (also called a transposon or jumping gene) is a mobile segment of DNA that can sometimes pick up a resistance gene and insert it into a plasmid or chromosome, thereby inducing horizontal gene transfer of antibiotic resistance.[40]

Horizontal transposon transfer (HTT) refers to the passage of pieces of DNA that are characterized by their ability to move from one locus to another between genomes by means other than parent-to-offspring inheritance. Horizontal gene transfer has long been thought to be crucial to prokaryotic evolution, but there is a growing amount of data showing that HTT is a common and widespread phenomenon in eukaryote evolution as well.[43] On the transposable element side, spreading between genomes via horizontal transfer may be viewed as a strategy to escape purging due to purifying selection, mutational decay and/or host defense mechanisms.[44]

HTT can occur with any type of transposable elements, but DNA transposons and LTR retroelements are more likely to be capable of HTT because both have a stable, double-stranded DNA intermediate that is thought to be sturdier than the single-stranded RNA intermediate of non-LTR retroelements, which can be highly degradable.[43] Non-autonomous elements may be less likely to transfer horizontally compared to autonomous elements because they do not encode the proteins required for their own mobilization. The structure of these non-autonomous elements generally consists of an intronless gene encoding a transposase protein, and may or may not have a promoter sequence. Those that do not have promoter sequences encoded within the mobile region rely on adjacent host promoters for expression.[43] Horizontal transfer is thought to play an important role in the TE life cycle.[43]

HTT has been shown to occur between species and across continents in both plants[45] and animals (Ivancevic et al. 2013), though some TEs have been shown to more successfully colonize the genomes of certain species over others.[46] Both spatial and taxonomic proximity of species has been proposed to favor HTTs in plants and animals.[45] It is unknown how the density of a population may affect the rate of HTT events within a population, but close proximity due to parasitism and cross contamination due to crowding have been proposed to favor HTT in both plants and animals.[45] Successful transfer of a transposable element requires delivery of DNA from donor to host cell (and to the germ line for multi-cellular organisms), followed by integration into the recipient host genome.[43] Though the actual mechanism for the transportation of TEs from donor cells to host cells is unknown, it is established that naked DNA and RNA can circulate in bodily fluid.[43] Many proposed vectors include arthropods, viruses, freshwater snails (Ivancevic et al. 2013), endosymbiotic bacteria,[44] and intracellular parasitic bacteria.[43] In some cases, even TEs facilitate transport for other TEs.[46]

The arrival of a new TE in a host genome can have detrimental consequences because TE mobility may induce mutation. However, HTT can also be beneficial by introducing new genetic material into a genome and promoting the shuffling of genes and TE domains among hosts, which can be co-opted by the host genome to perform new functions.[46] Moreover, transposition activity increases the TE copy number and generates chromosomal rearrangement hotspots.[47] HTT detection is a difficult task because it is an ongoing phenomenon that is constantly changing in frequency of occurrence and composition of TEs inside host genomes. Furthermore, few species have been analyzed for HTT, making it difficult to establish patterns of HTT events between species. These issues can lead to the underestimation or overestimation of HTT events between ancestral and current eukaryotic species.[47]

Methods of detection

Xenology
A speciation event produces orthologs of a gene in the two daughter species. A horizontal gene transfer event from one species to another adds a xenolog of the gene to the receiving genome.

Horizontal gene transfer is typically inferred using bioinformatics methods, either by identifying atypical sequence signatures ("parametric" methods) or by identifying strong discrepancies between the evolutionary history of particular sequences compared to that of their hosts. The transferred gene (xenolog) found in the receiving species is more closely related to the genes of the donor species than would be expected.

Viruses

The virus called Mimivirus infects amoebae. Another virus, called Sputnik, also infects amoebae, but it cannot reproduce unless mimivirus has already infected the same cell.[48] "Sputnik's genome reveals further insight into its biology. Although 13 of its genes show little similarity to any other known genes, three are closely related to mimivirus and mamavirus genes, perhaps cannibalized by the tiny virus as it packaged up particles sometime in its history. This suggests that the satellite virus could perform horizontal gene transfer between viruses, paralleling the way that bacteriophages ferry genes between bacteria."[49] Horizontal transfer is also seen between geminiviruses and tobacco plants.[50]

Prokaryotes

Horizontal gene transfer is common among bacteria, even among very distantly related ones. This process is thought to be a significant cause of increased drug resistance[5][51] when one bacterial cell acquires resistance, and the resistance genes are transferred to other species.[52][53] Transposition and horizontal gene transfer, along with strong natural selective forces have led to multi-drug resistant strains of S. aureus and many other pathogenic bacteria.[40] Horizontal gene transfer also plays a role in the spread of virulence factors, such as exotoxins and exoenzymes, amongst bacteria.[5] A prime example concerning the spread of exotoxins is the adaptive evolution of Shiga toxins in E. coli through horizontal gene transfer via transduction with Shigella species of bacteria.[54] Strategies to combat certain bacterial infections by targeting these specific virulence factors and mobile genetic elements have been proposed.[12] For example, horizontally transferred genetic elements play important roles in the virulence of E. coli, Salmonella, Streptococcus and Clostridium perfringens.[5]

In prokaryotes, restriction-modification systems are known to provide immunity against horizontal gene transfer and in stabilizing mobile genetic elements. Genes encoding restriction modification systems have been reported to move between prokaryotic genomes within mobile genetic elements such as plasmids, prophages, insertion sequences/transposons, integrative conjugative elements (ICEs), and integrons. Still, they are more frequently a chromosomal-encoded barrier to MGEs than an MGE-encoded tool for cell infection.[55]

Bacterial transformation

Transformation HGT in Bacteria
1: Donor bacteria 2: Bacteria who will receive the gene 3: The red portion represents the gene that will be transferred. Transformation in bacteria in a certain environment.

Natural transformation is a bacterial adaptation for DNA transfer (HGT) that depends on the expression of numerous bacterial genes whose products are responsible for this process.[56][57] In general, transformation is a complex, energy-requiring developmental process. In order for a bacterium to bind, take up and recombine exogenous DNA into its chromosome, it must become competent, that is, enter a special physiological state. Competence development in Bacillus subtilis requires expression of about 40 genes.[58] The DNA integrated into the host chromosome is usually (but with infrequent exceptions) derived from another bacterium of the same species, and is thus homologous to the resident chromosome. The capacity for natural transformation occurs in at least 67 prokaryotic species.[57] Competence for transformation is typically induced by high cell density and/or nutritional limitation, conditions associated with the stationary phase of bacterial growth. Competence appears to be an adaptation for DNA repair.[59] Transformation in bacteria can be viewed as a primitive sexual process, since it involves interaction of homologous DNA from two individuals to form recombinant DNA that is passed on to succeeding generations. Although transduction is the form of HGT most commonly associated with bacteriophages, certain phages may also be able to promote transformation.[60]

Bacterial conjugation

Conjugation HGT in Bacteria
1: Donor bacteria cell (F+ cell) 2: Bacteria that receives the plasmid (F- cell) 3: Plasmid that will be moved to the other bacteria 4: Pilus. Conjugation in bacteria using a sex pilus; then the bacteria that received the plasmid can go give it to other bacteria as well.

Conjugation in Mycobacterium smegmatis, like conjugation in E. coli, requires stable and extended contact between a donor and a recipient strain, is DNase resistant, and the transferred DNA is incorporated into the recipient chromosome by homologous recombination. However, unlike E. coli high frequency of recombination conjugation (Hfr), mycobacterial conjugation is a type of HGT that is chromosome rather than plasmid based.[61] Furthermore, in contrast to E. coli (Hfr) conjugation, in M. smegmatis all regions of the chromosome are transferred with comparable efficiencies. Substantial blending of the parental genomes was found as a result of conjugation, and this blending was regarded as reminiscent of that seen in the meiotic products of sexual reproduction.[61][62]

Archaeal DNA transfer

The archaeon Sulfolobus solfataricus, when UV irradiated, strongly induces the formation of type IV pili which then facilitates cellular aggregation.[63][64] Exposure to chemical agents that cause DNA damage also induces cellular aggregation.[63] Other physical stressors, such as temperature shift or pH, do not induce aggregation, suggesting that DNA damage is a specific inducer of cellular aggregation.

UV-induced cellular aggregation mediates intercellular chromosomal HGT marker exchange with high frequency,[65] and UV-induced cultures display recombination rates that exceed those of uninduced cultures by as much as three orders of magnitude. S. solfataricus cells aggregate preferentially with other cells of their own species.[65] Frols et al.[63][66] and Ajon et al.[65] suggested that UV-inducible DNA transfer is likely an important mechanism for providing increased repair of damaged DNA via homologous recombination. This process can be regarded as a simple form of sexual interaction.

Another thermophilic species, Sulfolobus acidocaldarius, is able to undergo HGT. S. acidocaldarius can exchange and recombine chromosomal markers at temperatures up to 84oC.[67] UV exposure induces pili formation and cellular aggregation.[65] Cells with the ability to aggregate have greater survival than mutants lacking pili that are unable to aggregate. The frequency of recombination is increased by DNA damage induced by UV-irradiation[68] and by DNA damaging chemicals.[69]

The ups operon, containing five genes, is highly induced by UV irradiation. The proteins encoded by the ups operon are employed in UV-induced pili assembly and cellular aggregation leading to intercellular DNA exchange and homologous recombination.[70] Since this system increases the fitness of S. acidocaldarius cells after UV exposure, Wolferen et al.[70][71] considered that transfer of DNA likely takes place in order to repair UV-induced DNA damages by homologous recombination.

Eukaryotes

"Sequence comparisons suggest recent horizontal transfer of many genes among diverse species including across the boundaries of phylogenetic 'domains'. Thus determining the phylogenetic history of a species can not be done conclusively by determining evolutionary trees for single genes."[72]

Organelle to nuclear genome

Bacteria to fungi

Bacteria to plants

  • Agrobacterium, a pathogenic bacterium that causes cells to proliferate as crown galls and proliferating roots is an example of a bacterium that can transfer genes to plants and this plays an important role in plant evolution.[75]

Endosymbiont to insects and nematodes

  • The adzuki bean beetle has acquired genetic material from its (non-beneficial) endosymbiont Wolbachia.[76] New examples have recently been reported demonstrating that Wolbachia bacteria represent an important potential source of genetic material in arthropods and filarial nematodes.[77]

Organelle to organelle

Plant to plant

  • Striga hermonthica, a parasitic eudicot, has received a gene from sorghum (Sorghum bicolor) to its nuclear genome.[81] The gene's functionality is unknown.
  • A gene that allowed ferns to survive in dark forests came from the hornwort, which grows in mats on streambanks or trees. The neochrome gene arrived about 180 million years ago.[82]

Fungi to insects

Human to protozoan

Bacteria to insects

  • HhMAN1 is a gene in the genome of the coffee borer beetle (Hypothenemus hampei) that resembles bacterial genes, and is thought to be transferred from bacteria in the beetle's gut.[86][87]

Viruses to plants

  • Plants are capable of receiving genetic information from viruses by horizontal gene transfer.[50]

Human genome

  • One study identified approximately 100 of humans' approximately 20,000 total genes which likely resulted from horizontal gene transfer,[88] but this number has been challenged by several researchers arguing these candidate genes for HGT are more likely the result of gene loss combined with differences in the rate of evolution[89]

Bacteria to animals

  • Bdelloid rotifers currently hold the 'record' for HGT in animals with ~8% of their genes from bacterial origins.[90] Tardigrades were thought to break the record with 17.5% HGT, but that finding was an artifact of bacterial contamination.[91]
  • A study found the genomes of 40 animals (including 10 primates, four Caenorhabditis worms, and 12 Drosophila insects) contained genes which the researchers concluded had been transferred from bacteria and fungi by horizontal gene transfer.[92] The researchers estimated that for some nematodes and Drosophilia insects these genes had been acquired relatively recently.[93]
  • A bacteriophage-mediated mechanism transfers genes between prokaryotes and eukaryotes. Nuclear localization signals in bacteriophage terminal proteins (TP) prime DNA replication and become covalently linked to the viral genome. The role of virus and bacteriophages in HGT in bacteria, suggests that TP-containing genomes could be a vehicle of inter-kingdom genetic information transference all throughout evolution.[94]

Plants to animals

Plant-fungus

  • Gene transfer between plants and fungi has been posited for a number of cases, including rice (Oryza sativa).

Artificial horizontal gene transfer

Artificial Bacterial Transformation
Before it is transformed, a bacterium is susceptible to antibiotics. A plasmid can be inserted when the bacteria is under stress, and be incorporated into the bacterial DNA creating antibiotic resistance. When the plasmids are prepared they are inserted into the bacterial cell by either making pores in the plasma membrane with temperature extremes and chemical treatments, or making it semi permeable through the process of electrophoresis, in which electric currents create the holes in the membrane. After conditions return to normal the holes in the membrane close and the plasmids are trapped inside the bacteria where they become part of the genetic material and their genes are expressed by the bacteria.

Genetic engineering is essentially horizontal gene transfer, albeit with synthetic expression cassettes. The Sleeping Beauty transposon system[98] (SB) was developed as a synthetic gene transfer agent that was based on the known abilities of Tc1/mariner transposons to invade genomes of extremely diverse species.[99] The SB system has been used to introduce genetic sequences into a wide variety of animal genomes.[100][101] (See also Gene therapy.)

Importance in evolution

Horizontal gene transfer is a potential confounding factor in inferring phylogenetic trees based on the sequence of one gene.[102] For example, given two distantly related bacteria that have exchanged a gene a phylogenetic tree including those species will show them to be closely related because that gene is the same even though most other genes are dissimilar. For this reason it is often ideal to use other information to infer robust phylogenies such as the presence or absence of genes or, more commonly, to include as wide a range of genes for phylogenetic analysis as possible.

For example, the most common gene to be used for constructing phylogenetic relationships in prokaryotes is the 16S ribosomal RNA gene since its sequences tend to be conserved among members with close phylogenetic distances, but variable enough that differences can be measured. However, in recent years it has also been argued that 16s rRNA genes can also be horizontally transferred. Although this may be infrequent, the validity of 16s rRNA-constructed phylogenetic trees must be reevaluated.[103]

Biologist Johann Peter Gogarten suggests "the original metaphor of a tree no longer fits the data from recent genome research" therefore "biologists should use the metaphor of a mosaic to describe the different histories combined in individual genomes and use the metaphor of a net to visualize the rich exchange and cooperative effects of HGT among microbes".[37] There exist several methods to infer such phylogenetic networks.

Using single genes as phylogenetic markers, it is difficult to trace organismal phylogeny in the presence of horizontal gene transfer. Combining the simple coalescence model of cladogenesis with rare HGT horizontal gene transfer events suggest there was no single most recent common ancestor that contained all of the genes ancestral to those shared among the three domains of life. Each contemporary molecule has its own history and traces back to an individual molecule cenancestor. However, these molecular ancestors were likely to be present in different organisms at different times."[104]

Challenge to the tree of life

Horizontal gene transfer poses a possible challenge to the concept of the last universal common ancestor (LUCA) at the root of the tree of life first formulated by Carl Woese, which led him to propose the Archaea as a third domain of life.[105] Indeed, it was while examining the new three-domain view of life that horizontal gene transfer arose as a complicating issue: Archaeoglobus fulgidus was seen as an anomaly with respect to a phylogenetic tree based upon the encoding for the enzyme HMGCoA reductase—the organism in question is a definite Archaean, with all the cell lipids and transcription machinery that are expected of an Archaean, but whose HMGCoA genes are of bacterial origin.[105] Scientists are broadly agreed on symbiogenesis, that mitochondria in eukaryotes derived from alpha-proteobacterial cells and that chloroplasts came from ingested cyanobacteria, and other gene transfers may have affected early eukaryotes. (In contrast, multicellular eukaryotes have mechanisms to prevent horizontal gene transfer, including separated germ cells.) If there had been continued and extensive gene transfer, there would be a complex network with many ancestors, instead of a tree of life with sharply delineated lineages leading back to a LUCA.[105][106] However, a LUCA can be identified, so horizontal transfers must have been relatively limited.[107]

Phylogenetic information in HGT

On the opposite, it has been remarked that the detection of Horizontal Gene Transfers could bring valuable phylogenetic and dating information.[108]

The potential of HGT to be used for dating phylogenies has recently been confirmed.[109][110]

The chromosomal organization of horizontal gene transfer

The acquisition of new genes has the potential to disorganize the other genetic elements and hinder the function of the bacterial cell, thus affecting the competitiveness of bacteria. Consequently, bacterial adaptation lies in a conflict between the advantages of acquiring beneficial genes, and the need to maintain the organization of the rest of its genome. Horizontally transferred genes are typically concentrated in only ~1% of the chromosome (in regions called hotspots). This concentration increases with genome size and with the rate of transfer. Hotspots diversify by rapid gene turnover; their chromosomal distribution depends on local contexts (neighboring core genes), and content in mobile genetic elements. Hotspots concentrate most changes in gene repertoires, reduce the trade-off between genome diversification and organization, and should be treasure troves of strain-specific adaptive genes. Most mobile genetic elements and antibiotic resistance genes are in hotspots, but many hotspots lack recognizable mobile genetic elements and exhibit frequent homologous recombination at flanking core genes. Overrepresentation of hotspots with fewer mobile genetic elements in naturally transformable bacteria suggests that homologous recombination and horizontal gene transfer are tightly linked in genome evolution.[111]

Genes

There is evidence for historical horizontal transfer of the following genes:

See also

Sources and notes

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Further reading

Ancestor

An ancestor is a parent or (recursively) the parent of an antecedent (i.e., a grandparent, great-grandparent, great-great-grandparent, and so forth). Ancestor is "any person from whom one is descended. In law the person from whom an estate has been inherited."Two individuals have a genetic relationship if one is the ancestor of the other, or if they share a common ancestor. In evolutionary theory, species which share an evolutionary ancestor are said to be of common descent. However, this concept of ancestry does not apply to some bacteria and other organisms capable of horizontal gene transfer. Some research suggests that the average person has twice as many female ancestors as male ancestors. This might have been due to the past prevalence of polygynous relations and female hypergamy.Assuming that all of an individual's ancestors are otherwise unrelated to each other, that individual has 2n ancestors in the nth generation before him and a total of 2g+1 − 2 ancestors in the g generations before him. In practice, however, it is clear that most ancestors of humans (and any other species) are multiply related (see pedigree collapse). Consider n = 40: the human species is mors, both living and dead; in contrast, some more youth-oriented cultural contexts display less veneration of elders. In other cultural contexts, some people seek providence from their deceased ancestors; this practice is sometimes known as ancestor worship or, more accurately, ancestor veneration.

Arborescent

Arborescent (French: arborescent) is a term used by the French thinkers Deleuze and Guattari to characterize thinking marked by insistence on totalizing principles, binarism, and dualism. The term, first used in A Thousand Plateaus (1980) where it was opposed to the rhizome, comes from the way genealogy trees are drawn: unidirectional progress, with no possible retroactivity and continuous binary cuts (thus enforcing a dualist metaphysical conception, criticized by Deleuze). Rhizomes, on the contrary, mark a horizontal and non-hierarchical conception, where anything may be linked to anything else, with no respect whatsoever for specific species: rhizomes are heterogeneous links between things that have nothing to do between themselves (for example, Deleuze and Guattari linked together desire and machines to create the - most surprising - concept of desiring machines). Horizontal gene transfer is also an example of rhizomes, opposed to the arborescent evolutionism theory. Deleuze also criticizes the Chomsky hierarchy of formal languages, which he considers a perfect example of arborescent dualistic theory.

Bdelloidea

Bdelloidea (Greek βδελλα, bdella, "leech-like") is a class of rotifers found in freshwater habitats all over the world. There are over 450 described species of bdelloid rotifers (or 'bdelloids'), distinguished from each other mainly on the basis of morphology. The main characteristics that distinguish bdelloids from related groups of rotifers are exclusively parthenogenetic reproduction and the ability to survive in dry, harsh environments by entering a state of desiccation-induced dormancy (anhydrobiosis) at any life stage. They are often referred to as "ancient asexuals" due to their unique asexual history that spans back to over 25 million years ago through fossil evidence. Bdelloid rotifers are microscopic organisms, typically between 150 and 700 µm in length. Most are slightly too small to be seen with the naked eye, but appear as tiny white dots through even a weak hand lens, especially in bright light.

CPS operon

The capsule biosynthesis, or CPS operon is a section of the genome present in some Escherichia coli which regulates the production of polysaccharides which make up the bacterial capsule. These polysaccharides help protect the bacteria from harsh environments, toxic chemicals, and bacteriophages.

The CPS operon contains genes which code for the following proteins:

Wza - a lipoprotein which may form a channel in the bacterial outer membrane.

Wzb - a cytoplasmic regulatory phosphatase which dephosphorylates Wzc.

Wzc - a tyrosine kinase found in the bacterial inner membrane. Participates in polymerization of capsule polysaccharides.

Wzx - Transfers new polysaccharide units across the inner membrane.

Wzy - Assembles longer polysaccharide chains using units introduced by Wzx.The CPS operon is likely transcriptionally regulated by the Rcs (regulation of capsule synthesis) proteins. Reduced levels of membrane-derived oligosaccharides result in autophosphorylation of RcsC. This results in a phosphate group being transferred from RcsC to RcsB. RcsB then binds to RcsA, forming a complex which acts on the CPS promoter and activates transcription of the CPS genes.

The same operon is present in Klebsiella species, possibly as a result of horizontal gene transfer.

EEF-1

eEF-1 is a eukaryotic elongation factor.

Its α and βγ subunits act as counterparts to EF-Tu and EF-Ts, respectively

Genes include:

EEF1A1, EEF1A2, EEF1A3

EEF1B2, and pseudogenes EEF1B2P1, EEF1B2P2, EEF1B2P3

EEF1D, EEF1E1, EEF1GVarious species of green algae, red algae, chromalveolates, and fungi lack the EF-1α gene but instead possess a related gene called EFL (elongation factor-like). Although its function has not been studied in depth, it appears to be similar to EF-1α.

Only two organisms are known to have both EF-1α and EFL: the fungus Basidiobolus and the diatom Thalassiosira. The evolutionary history of EFL is unclear. It may have arisen one or more times followed by loss of EFL or EF-1α. The presence in three diverse eukaryotic groups (fungi, chromalveolates, and archaeplastida) is supposed to be the result of two or more horizontal gene transfer events.

Gene cassette

A gene cassette is a type of mobile genetic element that contains a gene and a recombination site. Each cassette usually contains a single gene and tend to be very small; on the order of 500–1000 base pairs. They may exist incorporated into an integron or freely as circular DNA. Gene cassettes can move around within an organism's genome or be transferred to another organism in the environment via horizontal gene transfer. These cassettes often carry antibiotic resistance genes. An example would be the kanMX cassette which confers kanamycin (an antibiotic) resistance upon bacteria.

Gene flow

In population genetics, gene flow (also known as gene migration or allele flow) is the transfer of genetic variation from one population to another. If the rate of gene flow is high enough, then two populations are considered to have equivalent allele frequencies and therefore effectively be a single population. It has been shown that it takes only "One migrant per generation" to prevent populations from diverging due to drift. Gene flow is an important mechanism for transferring genetic diversity among populations. Migrants change the distribution of genetic diversity within the populations, by modifying the allele frequencies (the proportion of members carrying a particular variant of a gene). High rates of gene flow can reduce the genetic differentiation between the two groups, increasing homogeneity. For this reason, gene flow has been thought to constrain speciation by combining the gene pools of the groups, thus preventing the development of differences in genetic variation that would have led to full speciation. In some cases migration may also result in the addition of novel genetic variants to the gene pool of a species or population.

There are a number of factors that affect the rate of gene flow between different populations. Gene flow is expected to be lower in species that have low dispersal or mobility, that occur in fragmented habitats, where there is long distances between populations, and when there are small population sizes. Mobility plays an important role in the migration rate, as highly mobile individuals tend to have greater migratory prospects. Although animals are thought to be more mobile than plants, pollen and seeds may be carried great distances by animals or wind. When gene flow is impeded, there can be an increase in inbreeding, measured by the inbreeding coefficient (F) within a population. For example, many island populations have low rates of gene flow due to geographic isolation and small population sizes. The Black Footed Rock Wallaby has several inbred populations that live on various islands off the coast of Australia. The population is so strongly isolated that lack of gene flow has led to high rates of inbreeding.

Horizontal gene transfer in evolution

Scientists trying to reconstruct evolutionary history have been challenged by the fact that genes can sometimes transfer between distant branches on the tree of life. This movement of genes can occur through horizontal gene transfer (HGT), scrambling the information on which biologists relied to reconstruct the phylogeny of organisms. Conversely, HGT can also help scientists to reconstruct and date the tree of life. Indeed, a gene transfer can be used as a phylogenetic marker, or as the proof of contemporaneity of the donor and recipient organisms, and as a trace of extinct biodiversity.

HGT happens very infrequently – at the individual organism level, it is highly improbable for any such event to take place. However, on the grander scale of evolutionary history, these events occur with some regularity. On one hand, this forces biologists to abandon the use of individual genes as good markers for the history of life. On the other hand, this provides an almost unexploited large source of information about the past.

Organism

In biology, an organism (from Greek: ὀργανισμός, organismos) is any individual entity that propagates the properties of life. It is a synonym for "life form".

Organisms are classified by taxonomy into specified groups such as the multicellular animals, plants, and fungi; or unicellular microorganisms such as a protists, bacteria, and archaea. All types of organisms are capable of reproduction, growth and development, maintenance, and some degree of response to stimuli. Humans are multicellular animals composed of many trillions of cells which differentiate during development into specialized tissues and organs.

An organism may be either a prokaryote or a eukaryote. Prokaryotes are represented by two separate domains – bacteria and archaea. Eukaryotic organisms are characterized by the presence of a membrane-bound cell nucleus and contain additional membrane-bound compartments called organelles (such as mitochondria in animals and plants and plastids in plants and algae, all generally considered to be derived from endosymbiotic bacteria). Fungi, animals and plants are examples of kingdoms of organisms within the eukaryotes.

Estimates on the number of Earth's current species range from 10 million to 14 million, of which only about 1.2 million have been documented. More than 99% of all species, amounting to over five billion species, that ever lived are estimated to be extinct. In 2016, a set of 355 genes from the last universal common ancestor (LUCA) of all organisms was identified.

Pathogenicity island

Pathogenicity islands (PAIs), as termed in 1990, are a distinct class of genomic islands acquired by microorganisms through horizontal gene transfer. Pathogenicity islands are found in both animal and plant pathogens. Additionally, PAIs are found in both gram-positive and gram-negative bacteria. They are transferred through horizontal gene transfer events such as transfer by a plasmid, phage, or conjugative transposon. Therefore, PAIs contribute to microorganisms' ability to evolve.

One species of bacteria may have more than one PAI. For example, Salmonella has at least five.

An analogous genomic structure in rhizobia is termed a symbiosis island.

Paulinella

Paulinella is a genus of about nine species of freshwater amoeboids.

Its most famous members are the three photosynthetic species P. chromatophora, P. micropora and P. longichromatophora, the first two being freshwater forms and the third a marine form, which has recently (in evolutionary terms) taken on a cyanobacterium as an endosymbiont. The plastid is often referred to as the 'cyanelle' or chromatophore. The endosymbiotic event happened about 100 million years in a bacterial species which diverged about 500 million years ago from some known cyanobacteria. This is striking because the chloroplasts of all other known photosynthetic eukaryotes derive ultimately from a single cyanobacterium endosymbiont, which was taken in probably over a billion years ago by an ancestral archaeplastidan (and subsequently adopted into other eukaryote groups, by further endosymbiosis events). The P. chromatophora symbiont was related to the Prochlorococcus and Synechococcus cyanobacteria (sister to the group consisting of the living members of those two genera). The chromatophore genome has gone through a reduction, and is now just one third the size of the genome of its closest free living relatives, but still 10-fold larger than most plastid genomes. Some of the genes have been lost, others have migrated to the amoeba's nucleus through endosymbiotic gene transfer. Other genes have degenerated due to Muller's ratchet - accumulations of harmful mutations due to genetic isolation, and have probably been replaced with genes from other microbes through horizontal gene transfer. The nuclear genes of P. chromatophora (those regions not modified by the symbiont) are most closely related to the heterotrophic P. ovalis. P. ovalis also have at least two cyanobacterial-like genes, which were probably integrated into their genome through horizontal gene transfer from its cyanobacterial prey. Similar genes could have made the photosynthetic speices pre-equipped to accept the chromatophore.

Plant–fungus horizontal gene transfer

Plant–fungus horizontal gene transfer is the movement of genetic material between individuals in the plant and fungus kingdoms. Horizontal gene transfer is universal in fungi, viruses, bacteria, and other eukaryotes. Horizontal gene transfer research often focuses on prokaryotes because of the abundant sequence data from diverse lineages, and because it is assumed not to play a significant role in eukaryotes.Most plant–fungus horizontal gene transfer events are ancient and rare, but they may have provided important gene functions leading to wider substrate use and habitat spread for plants and fungi. Since these events are rare and ancient, they have been difficult to detect and remain relatively unknown. Plant–fungus interactions could play a part in a multi-horizontal gene transfer pathway among many other organisms.

Plasmid

A plasmid is a small DNA molecule within a cell that is physically separated from chromosomal DNA and can replicate independently. They are most commonly found as small circular, double-stranded DNA molecules in bacteria; however, plasmids are sometimes present in archaea and eukaryotic organisms. In nature, plasmids often carry genes that benefit the survival of the organism, such as by providing antibiotic resistance. While the chromosomes are big and contain all the essential genetic information for living under normal conditions, plasmids usually are very small and contain only additional genes that may be useful in certain situations or conditions. Artificial plasmids are widely used as vectors in molecular cloning, serving to drive the replication of recombinant DNA sequences within host organisms. In the laboratory, plasmids may be introduced into a cell via transformation.

Plasmids are considered replicons, units of DNA capable of replicating autonomously within a suitable host. However, plasmids, like viruses, are not generally classified as life. Plasmids are transmitted from one bacterium to another (even of another species) mostly through conjugation. This host-to-host transfer of genetic material is one mechanism of horizontal gene transfer, and plasmids are considered part of the mobilome. Unlike viruses, which encase their genetic material in a protective protein coat called a capsid, plasmids are "naked" DNA and do not encode genes necessary to encase the genetic material for transfer to a new host. However, some classes of plasmids encode the conjugative "sex" pilus necessary for their own transfer. The size of the plasmid varies from 1 to over 200 kbp, and the number of identical plasmids in a single cell can range anywhere from one to thousands under some circumstances.

The relationship between microbes and plasmid DNA is neither parasitic nor mutualistic, because each implies the presence of an independent species living in a detrimental or commensal state with the host organism. Rather, plasmids provide a mechanism for horizontal gene transfer within a population of microbes and typically provide a selective advantage under a given environmental state. Plasmids may carry genes that provide resistance to naturally occurring antibiotics in a competitive environmental niche, or the proteins produced may act as toxins under similar circumstances, or allow the organism to utilize particular organic compounds that would be advantageous when nutrients are scarce.

Rafflesiaceae

The Rafflesiaceae are a family of rare parasitic plants found in the tropical forests of east and southeast Asia, including Rafflesia arnoldii, which has the largest flowers of all plants. The plants are endoparasites of vines in the genus Tetrastigma (Vitaceae) and lack stems, leaves, roots, and any photosynthetic tissue. They rely entirely on their host plants for both water and nutrients, and only then emerge as flowers from the roots or lower stems of the host plants.

Thermoacidophile

A thermoacidophile is an extremophilic microorganism that is both thermophilic and acidophilic; i.e., it can grow under conditions of high temperature and low pH. The large majority of thermoacidophiles are archaea (particularly the crenarchaeota and euryarchaeota) or bacteria, though occasional eukaryotic examples have been reported. Thermoacidophiles can be found in hot springs and solfataric environments, within deep sea vents, or in other environments of geothermal activity. They also occur in polluted environments, such as in acid mine drainage.An apparent tradeoff has been described between adaptation to high temperature and low pH; relatively few examples are known that are tolerant of the extremes of both environments (pH < 2, growth temperature > 80°C). Many thermoacidophilic archaea have aerobic or microaerophilic metabolism, although obligately anaerobic examples (e.g. the Acidilobales) have also been identified.Sequencing the genome of a thermoacidophilic eukaryote, the red algae Galdieria sulphuraria, revealed that its environmental adaptations likely originated from horizontal gene transfer from thermoacidophilic archaea and bacteria.

Torulene

Torulene (3',4'-didehydro-β,γ-carotene) is a carotene (a hydrocarbon carotenoid) which is notable for being synthesized by red pea aphids (Acyrthosiphon pisum), imparting the natural red color to the aphids, which aids in their camouflage and escape from predation. The aphids have gained the ability to synthesize torulene by horizontal gene transfer of a number of genes for carotenoid synthesis, apparently from fungi. Plants, fungi, and microorganisms can synthesize carotenoids, but torulene made by pea aphids is the only carotenoid known to be synthesized by an organism in the animal kingdom.

Transmission (genetics)

Genetic transmission is the transfer of genetic information from genes to another generation (from parent to offspring), almost synonymous with heredity, or from one location in a cell to another.

It should not be confused with chromosomal translocation, which is rearrangement of parts between non-homologous chromosomes.

It should also not be confused with horizontal gene transfer, a process in which an organism incorporates genetic material from another organism without being the offspring of that organism.

Tree of life (biology)

The tree of life or universal tree of life is a metaphor, model and research tool used to explore the evolution of life and describe the relationships between organisms, both living and extinct, as described in a famous passage in Charles Darwin's On the Origin of Species (1859).

The affinities of all the beings of the same class have sometimes been represented by a great tree. I believe this simile largely speaks the truth.

Tree diagrams originated in the medieval era to represent genealogical relationships.

Phylogenetic tree diagrams in the evolutionary sense date back to at least the early 19th century.

The term phylogeny for the evolutionary relationships of species through time was coined by Ernst Haeckel, who went further than Darwin in proposing phylogenic histories of life. In contemporary usage, tree of life refers to the compilation of comprehensive phylogenetic databases rooted at the last universal common ancestor of life on Earth. The Open Tree of Life, first published 2015, is a project to compile such a database for free public access.

Trex

Trex or T-Rex may refer to:

Tyrannosaurus rex, a large dinosaur species

Trex Company, a composite decking manufacturer

TREX Regional Exchanges Oy (IXP), an Internet Exchange Point in Finland

Trex (card game) a card game

TREX, a search engine in SAP NetWeaver

TREX (Tree Regular Expressions for XML)

T-REX (webserver), a webserver for phylogenetic inference, visualization and horizontal gene transfer detection

The proteins TREX1 and TREX2

Primarily prokaryotic
Occurs in eukaryotes
Viral

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