Biology:Horizontal gene transfer

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Short description: Type of nonhereditary genetic change
Tree of life showing vertical and horizontal gene transfers

Horizontal gene transfer (HGT) or lateral gene transfer (LGT)[1][2][3] is the movement of genetic material between 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] HGT is influencing scientific understanding of higher order evolution while more significantly shifting perspectives on bacterial evolution.[7]

Horizontal gene transfer is the primary mechanism for the spread of antibiotic resistance in bacteria,[8][5][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 a challenge to manage in the field of medicine. Ecological factors may also play a role in the HGT of antibiotic resistant genes.[16]

Horizontal gene transfer is recognized as a pervasive evolutionary process that distributes genes between divergent prokaryotic lineages[17] and can also involve eukaryotes.[18][19] It is postulated that HGT promotes the maintenance of a universal life biochemistry and, subsequently, the universality of the genetic code.[20]

History

Griffith's experiment, reported in 1928 by Frederick Griffith,[21] was the first experiment suggesting that bacteria are capable of transferring genetic information through a process known as transformation.[22][23] Griffith's findings were followed by research in the late 1930s and early 1940s 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,[24] simultaneously revealing the mechanism of diphtheria (that patients could be infected with the bacteria but not have any symptoms, and then suddenly convert later or never),[25] and giving the first example for the relevance of the lysogenic cycle.[26] 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.[27][28] In the mid-1980s, Syvanen[29] postulated that biologically significant lateral gene transfer has existed since the beginning of life on Earth and has been involved in shaping all of evolutionary history.

As Jian, Rivera and Lake (1999) put it: "Increasingly, studies of genes and genomes are indicating that considerable horizontal transfer has occurred between prokaryotes"[30] (see also Lake and Rivera, 2007).[31] 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."[32]

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.[33] Some Lepidoptera (e.g. monarch butterflies and silkworms) have been genetically modified by horizontal gene transfer from the wasp bracovirus.[34] Bites from insects in the family Reduviidae (assassin bugs) can, via a parasite, infect humans with the trypanosomal Chagas disease, which can insert its DNA into the human genome.[35] It has been suggested that lateral gene transfer to humans from bacteria may play a role in cancer.[36]

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."[37]

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".[38]

Mechanisms

There are several mechanisms for horizontal gene transfer:[5][39][40]

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.[41]

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.[44] 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.[45]

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.[44] 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.[44] Horizontal transfer is thought to play an important role in the TE life cycle.[44] In plants, it appears that LTR retrotransposons of the Copia superfamilies, especially those with low copy numbers from the Ale and Ivana lineages, are more likely to undergo horizontal transfer between different plant species.[46]

HTT has been shown to occur between species and across continents in both plants[47] and animals (Ivancevic et al. 2013), though some TEs have been shown to more successfully colonize the genomes of certain species over others.[48] Both spatial and taxonomic proximity of species has been proposed to favor HTTs in plants and animals.[47] 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.[47] In plants, the interaction between lianas and trees has been shown to facilitate HTT in natural ecosystems.[49] 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.[44] 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.[44] Many proposed vectors include arthropods, viruses, freshwater snails (Ivancevic et al. 2013), endosymbiotic bacteria,[45] and intracellular parasitic bacteria.[44] In some cases, even TEs facilitate transport for other TEs.[48]

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.[48] Moreover, transposition activity increases the TE copy number and generates chromosomal rearrangement hotspots.[50] 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.[50]

Methods of detection

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.
Main page: Biology:Inferring horizontal gene transfer

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.[citation needed]

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.[51]

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.[52]

Horizontal transfer is also seen between geminiviruses and tobacco plants.

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][53] when one bacterial cell acquires resistance, and the resistance genes are transferred to other species.[54][55] 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.[41] 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.[56] 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 (MGE) such as plasmids, prophages, insertion sequences/transposons, integrative conjugative elements (ICE),[57] and integrons. Still, they are more frequently a chromosomal-encoded barrier to MGE than an MGE-encoded tool for cell infection.[58]

Lateral gene transfer via a mobile genetic element, namely the integrated conjugative element (ICE) Bs1 has been reported for its role in the global DNA damage SOS response of the gram positive Bacillus subtilis.[59] Furthermore, it has been linked with the radiation and desiccation resistance of Bacillus pumilus SAFR-032 spores,Cite error: Closing </ref> missing for <ref> tagCite error: Closing </ref> missing for <ref> tag This is clearly exhibited within certain groups of bacteria including P. aeruginosa and actinomycetales, an order of Actinomycetota.[citation needed] Polyketide synthases (PKSs) and biosynthetic gene clusters provide modular organizations of associated genes making these bacteria well-adapted to acquire and discard helpful modular modifications via HGT.[citation needed] Certain areas of genes known as hotspots further increase the likelihood of horizontally transferred secondary metabolite-producing genes.[60] The promiscuity of enzymes is a reoccurring theme in this particular theatre.[citation needed]

Bacterial transformation

1: Donor bacteria 2: Bacteria who will receive the gene 3: The red portion represents the gene that will be transferred. Transformation in bacteria happens 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.[61][62] 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.[63] 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.[62] 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.[64] 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.[65]

Bacterial conjugation

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.[66] 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.[66][67]

Archaeal DNA transfer

Haloarchaea are aerobic halophiles thought to have evolved from anaerobic methanogens. A large amount of their genome, 126 composite gene families, are derived from genetic material from bacterial genomes. This has allowed them to adapt to extremely salty environments.[68][69]

The archaeon Sulfolobus solfataricus, when UV irradiated, strongly induces the formation of type IV pili which then facilitates cellular aggregation.[70][71] Exposure to chemical agents that cause DNA damage also induces cellular aggregation.[70] Other physical stressors, such as temperature shift or pH, do not induce aggregation, suggesting that DNA damage is a specific inducer of cellular aggregation.[citation needed]

UV-induced cellular aggregation mediates intercellular chromosomal HGT marker exchange with high frequency,[72] 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.[72] Frols et al.[70][73] and Ajon et al.[72] 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 84 °C.[74] UV exposure induces pili formation and cellular aggregation.[72] 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[75] and by DNA damaging chemicals.[76]

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.[77] Since this system increases the fitness of S. acidocaldarius cells after UV exposure, Wolferen et al.[77][78] 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."[79]

Organelle to nuclear genome

  • Analysis of DNA sequences suggests that horizontal gene transfer has occurred within eukaryotes from the chloroplast and mitochondrial genomes to the nuclear genome. As stated in the endosymbiotic theory, chloroplasts and mitochondria probably originated as bacterial endosymbionts of a progenitor to the eukaryotic cell.[80]

Organelle to organelle

  • Mitochondrial genes moved to parasites of the Rafflesiaceae plant family from their hosts[81][82] and from chloroplasts of a still-unidentified plant to the mitochondria of the bean Phaseolus.[83]

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.[85]

Bacteria to insects

  • HhMAN1 is a gene in the genome of the coffee berry borer (Hypothenemus hampei) that resembles bacterial genes, and is thought to be transferred from bacteria in the beetle's gut.[86][87]
  • oskar is an essential gene for the specification of the germline in Holometabola and its origin is through to be due to a HGT event followed by a fusion with a LOTUS domain.[88]

Bacteria to animals

  • Bdelloid rotifers currently hold the 'record' for HGT in animals with ~8% of their genes from bacterial origins.[89] Tardigrades were thought to break the record with 17.5% HGT, but that finding was an artifact of bacterial contamination.[90]
  • 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.[91] The researchers estimated that for some nematodes and Drosophila insects these genes had been acquired relatively recently.[92]
  • A bacteriophage-mediated mechanism transfers genes between prokaryotes and eukaryotes.[93] 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]

Endosymbiont to insects and nematodes

  • The adzuki bean beetle has acquired genetic material from its (non-beneficial) endosymbiont Wolbachia.[95] New examples have recently been reported demonstrating that Wolbachia bacteria represent an important potential source of genetic material in arthropods and filarial nematodes.[96]
  • The psyllid Pachypsylla venusta has acquired genes from its current endosymbiont Carsonella, and from many of its historical endosymbionts, too.[97]

Plant to plant

  • Striga hermonthica, a parasitic eudicot, has received a gene from sorghum (Sorghum bicolor) to its nuclear genome.[98] 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.[99]

Plants to animals

Plant to fungus

  • Gene transfer between plants and fungi has been posited for a number of cases, including rice (Oryza sativa).[citation needed]
  • Evidence of gene transfer from plants was documented in the fungus Colletotrichum.[104]
  • Plant expansin genes were transferred to fungi further enabling the fungi to infect plants.[105]

Plant to bacteria

  • Plant expansin genes were transferred to bacteria further enabling the bacteria to infect plants.[105]

Fungi to insects

Fungi to fungi

  • The toxin α-amanitin is found in numerous, seemingly unrelated genera fungi such as Amanita, Lepiota, and Galerina. Two biosynthetic genes involved in the production of α-amanitin are P450-29 and FMO1. Phylogenetic and genetic analyses of these genes strongly indicate that they were transferred between the genera via horizontal gene transfer.[108]

Animals to animals

Animals to bacteria

  • The strikingly fish-like copper/zinc superoxide dismutase of Photobacterium leiognathi[110] is most easily explained in terms of transfer of a gene from an ancestor of its fish host.

Human to protozoan

Human genome

  • One study identified approximately 100 of humans' approximately 20,000 total genes which likely resulted from horizontal gene transfer,[112] 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.[113]

Compounds found to promote horizontal gene transfer

Through research into the growing issue of antibiotic resistance[114] certain compounds have been observed to promote horizontal gene transfer.[115][116][117][118] Antibiotics given to bacteria at non-lethal levels have been known to be a cause of antibiotic resistance[118] but emerging research is now showing that certain non-antibiotic pharmaceuticals (ibuprofen, naproxen, gemfibrozil, diclofenac, propranolol, etc.) also have a role in promoting antibiotic resistance through their ability to promote horizontal gene transfer (HGT) of genes responsible for antibiotic resistance. The transfer of antibiotic resistance genes (ARGs) through conjugation is significantly accelerated when donor cells with plasmids and recipient cells are introduced to each other in the presence of one of the pharmaceuticals.[115] Non-antibiotic pharmaceuticals were also found to cause some responses in bacteria similar to those responses to antibiotics, such as increasing expression of the genes lexA, umuC, umuD and soxR involved in the bacteria's SOS response as well as other genes also expressed during exposure to antibiotics.[115] These findings are from 2021 and due to the widespread use of non-antibiotic pharmaceuticals, more research needs to be done in order to further understanding on the issue.[115]

Alongside non-antibiotic pharmaceuticals, other compounds relevant to antibiotic resistance have been tested such as malachite green, ethylbenzene, styrene, 2,4-dichloroaniline, trioxymethylene, o-xylene solutions, p-nitrophenol (PNP), p-aminophenol (PAP), and phenol (PhOH).[116][117] It is a global concern that ARGs have been found in wastewater treatment plants[116] Textile wastewater has been found to contain 3- to 13-fold higher abundance of mobile genetic elements than other samples of wastewater.[116] The cause of this is the organic compounds used for textile dying (o-xylene, ethylbenzene, trioxymethylene, styrene, 2,4-dichloroaniline, and malachite green)[116] raising the frequency of conjugative transfer when bacteria and plasmid (with donor) are introduced in the presence of these molecules.[116] When textile wastewater combines with wastewater from domestic sewage, the ARGs present in wastewater are transferred at a higher rate due to the addition of textile dyeing compounds increasing the occurrence of HGT.[citation needed]

Other organic pollutants commonly found in wastewater have been the subject of similar experiments.[117] A 2021 study used similar methods of  using plasmid in a donor and mixing that with a receptor in the presence of compound in order to test horizontal gene transfer of antibiotic resistance genes but this time in the presence of phenolic compounds.[117] Phenolic compounds are commonly found in wastewater and have been found to change functions and structures of the microbial communities during the wastewater treatment process.[117] Additionally, HGT increases in frequency in the presence of the compounds p-nitrophenol (PNP), p-aminophenol (PAP), and phenol. These compounds result in a 2- to 9-fold increase in HGT (p-nitrophenol being on the lower side of 2-fold increases and p-aminophenol and phenol having a maximum increase of 9-fold).[117] This increase in HGT is on average less than the compounds ibuprofen, naproxen, gemfibrozil, diclofenac, propranolol, o-xylene, ethylbenzene, trioxymethylene, styrene, 2,4-dichloroaniline, and malachite green[115][116] but their increases is still significant.[117] The study that came to this conclusion is similar to the study on horizontal gene transfer and non-antibiotic pharmaceuticals in that it was done in 2021 and leaves room for more research, specifically in the focus of the study which is activated sludge.[117]

Heavy metals have also been found to promote conjugative transfer of antibiotic resistance genes.[118] The paper that led to the discovery of this was done in 2017 during the emerging field of horizontal gene transfer assisting compound research.[118] Metals assist in the spread of antibiotic resistance through both co-resistance as well as cross-resistance mechanisms.[118] In quantities relevant to the environment, Cu(II), Ag(I), Cr(VI), and Zn(II) promote HGT from donor and receptor strains of E. coli.[118] The presence of these metals triggered SOS response from bacterial cells and made the cells more permeable. These are the mechanisms that make even low levels of heavy metal pollution in the environment impact HGT and therefore the spread of ARGs.

Artificial horizontal gene transfer

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[119] (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.[120] The SB system has been used to introduce genetic sequences into a wide variety of animal genomes.[121][122]

In evolution

Main page: Biology:Horizontal gene transfer in evolution

Horizontal gene transfer is a potential confounding factor in inferring phylogenetic trees based on the sequence of one gene.[123] 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.[124]

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".[38] 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."[125]

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.[126] 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.[126] 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.[126][127] However, a LUCA can be identified, so horizontal transfers must have been relatively limited.[128]

Other early HGTs are thought to have happened. The first common ancestor (FUCA), earliest ancestor of LUCA, had other descendants that had their own lineages.[129] These now-extinct sister lineages of LUCA descending from FUCA are thought to have horizontally transferred some of their genes into the genome of early descendants of LUCA.[129]

Phylogenetic information in HGT

It has been remarked that, despite the complications, the detection of horizontal gene transfers brings valuable phylogenetic and dating information.[130]

The potential of HGT to be used for dating phylogenies has recently been confirmed.[131][132]

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.[133]

Genes

This list is incomplete; you can help by expanding it.

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

See also


References

  1. ↑ "Lateral gene transfer and the nature of bacterial innovation". Nature 405 (6784): 299–304. May 2000. doi:10.1038/35012500. PMID 10830951. Bibcode: 2000Natur.405..299O. 
  2. ↑ "Horizontal gene transfer between bacteria and animals". Trends in Genetics 27 (4): 157–63. April 2011. doi:10.1016/j.tig.2011.01.005. PMID 21334091. 
  3. ↑ "A review of bacteria-animal lateral gene transfer may inform our understanding of diseases like cancer". PLOS Genetics 9 (10): e1003877. October 2013. doi:10.1371/journal.pgen.1003877. PMID 24146634. 
  4. ↑ "Horizontal gene transfer in eukaryotic evolution". Nature Reviews. Genetics 9 (8): 605–18. August 2008. doi:10.1038/nrg2386. PMID 18591983. 
  5. ↑ 5.0 5.1 5.2 5.3 5.4 5.5 "Horizontally transferred genetic elements and their role in pathogenesis of bacterial disease". Veterinary Pathology 51 (2): 328–40. March 2014. doi:10.1177/0300985813511131. PMID 24318976. 
  6. ↑ "Speciation through the looking-glass". Biological Journal of the Linnean Society 120 (2): 480–488. 2017. doi:10.1111/bij.12872. 
  7. ↑ "Examining bacterial species under the specter of gene transfer and exchange". Proceedings of the National Academy of Sciences of the United States of America 102 (Suppl 1): 6595–6599. May 2005. doi:10.1073/pnas.0502035102. PMID 15851673. Bibcode: 2005PNAS..102.6595O. 
  8. ↑ "Horizontal gene transfer in the human gastrointestinal tract: potential spread of antibiotic resistance genes". Infection and Drug Resistance 7: 167–176. 2014. doi:10.2147/idr.s48820. PMID 25018641. 
  9. ↑ "Horizontal gene transfer in prokaryotes: quantification and classification". Annual Review of Microbiology 55 (1): 709–42. 2001. doi:10.1146/annurev.micro.55.1.709. PMID 11544372. 
  10. ↑ "Barriers to horizontal gene transfer by natural transformation in soil bacteria". APMIS 84 (S84): 77–84. 1998. doi:10.1111/j.1600-0463.1998.tb05653.x. PMID 9850687. 
  11. ↑ "Evidence for interspecies gene transfer in the evolution of 2,4-dichlorophenoxyacetic acid degraders". Applied and Environmental Microbiology 64 (10): 4089–92. October 1998. doi:10.1128/AEM.64.10.4089-4092.1998. PMID 9758850. Bibcode: 1998ApEnM..64.4089M. 
  12. ↑ 12.0 12.1 "Paradigms of pathogenesis: targeting the mobile genetic elements of disease". Frontiers in Cellular and Infection Microbiology 2: 161. December 2012. doi:10.3389/fcimb.2012.00161. PMID 23248780. 
  13. ↑ "Transfer of broad-host-range antibiotic resistance plasmids in soil microcosms". Curr. Microbiol. 28 (4): 209–215. 1994. doi:10.1007/BF01575963. 
  14. ↑ "Efficient transfer of antibiotic resistance plasmids by transduction within methicillin-resistant Staphylococcus aureus USA300 clone". FEMS Microbiology Letters 332 (2): 146–52. July 2012. doi:10.1111/j.1574-6968.2012.02589.x. PMID 22553940. 
  15. ↑ "Molecular characterization of a new efficiently transducing bacteriophage identified in meticillin-resistant Staphylococcus aureus". The Journal of General Virology 97 (1): 258–268. January 2016. doi:10.1099/jgv.0.000329. PMID 26537974. 
  16. ↑ "Ecology determines how low antibiotic concentration impacts community composition and horizontal transfer of resistance genes". Communications Biology 1 (1): 35. 2018-04-19. doi:10.1038/s42003-018-0041-7. PMID 30271921. 
  17. ↑ "Functions predict horizontal gene transfer and the emergence of antibiotic resistance". Science Advances 7 (43): eabj5056. October 2021. doi:10.1126/sciadv.abj5056. PMID 34678056. Bibcode: 2021SciA....7.5056Z. 
  18. ↑ "Lateral gene transfer between prokaryotes and eukaryotes". Experimental Cell Research 358 (2): 421–426. September 2017. doi:10.1016/j.yexcr.2017.02.009. PMID 28189637. 
  19. ↑ "Origin and Early Evolution of the Eukaryotic Cell". Annual Review of Microbiology 75 (1): 631–647. October 2021. doi:10.1146/annurev-micro-090817-062213. PMID 34343017. 
  20. ↑ "On universal coding events in protein biogenesis". Bio Systems 164: 16–25. February 2018. doi:10.1016/j.biosystems.2017.10.004. PMID 29030023. Bibcode: 2018BiSys.164...16K. 
  21. ↑ "The Significance of Pneumococcal Types". The Journal of Hygiene (Cambridge University Press) 27 (2): 113–59. January 1928. doi:10.1017/S0022172400031879. PMID 20474956. 
  22. ↑ "Bacterial gene transfer by natural genetic transformation in the environment". Microbiological Reviews 58 (3): 563–602. September 1994. doi:10.1128/MMBR.58.3.563-602.1994. PMID 7968924. 
  23. ↑ "Pneumococcal transformation--a backward view. Fourth Griffith Memorial Lecture". Journal of General Microbiology 73 (1): 1–11. November 1972. doi:10.1099/00221287-73-1-1. PMID 4143929. http://mic.sgmjournals.org/content/73/1/1.full.pdf. 
  24. ↑ "Studies on the virulence of bacteriophage-infected strains of Corynebacterium diphtheriae". Journal of Bacteriology 61 (6): 675–88. June 1951. doi:10.1128/JB.61.6.675-688.1951. PMID 14850426. 
  25. ↑ Phillip Marguilies "Epidemics: Deadly diseases throughout history". Rosen, New York. 2005.
  26. ↑ André Lwoff (1965). "Interaction among Virus, Cell, and Organism". Nobel Lecture for the Nobel Prize in Physiology or Medicine.
  27. ↑ "Inheritance of drug resistance (and its transfer) between Shigella strains and Between Shigella and E. coli strains" (in ja). Hihon Iji Shimpor 1861: 34. 1959. 
  28. ↑ "On the mechanism of the development of multiple-drug-resistant clones of Shigella". Japanese Journal of Microbiology 4 (2): 219–27. April 1960. doi:10.1111/j.1348-0421.1960.tb00170.x. PMID 13681921. 
  29. ↑ "Cross-species gene transfer; implications for a new theory of evolution". Journal of Theoretical Biology 112 (2): 333–43. January 1985. doi:10.1016/S0022-5193(85)80291-5. PMID 2984477. Bibcode: 1985JThBi.112..333S. http://www.dcn.davis.ca.us/vme/hgt/JTheoBiolvol112pp333-343yr1985.PDF. 
  30. ↑ "Horizontal gene transfer among genomes: the complexity hypothesis". Proceedings of the National Academy of Sciences of the United States of America 96 (7): 3801–6. March 1999. doi:10.1073/pnas.96.7.3801. PMID 10097118. Bibcode: 1999PNAS...96.3801J. 
  31. ↑ "The ring of life provides evidence for a genome fusion origin of eukaryotes". Nature 431 (7005): 152–5. September 2004. doi:10.1038/nature02848. PMID 15356622. Bibcode: 2004Natur.431..152R. http://www.sdsc.edu/~shindyal/ejc121304.pdf. 
  32. ↑ "Do orthologous gene phylogenies really support tree-thinking?". BMC Evolutionary Biology 5 (1): 33. May 2005. doi:10.1186/1471-2148-5-33. PMID 15913459. Bibcode: 2005BMCEE...5...33B. 
  33. ↑ "Farmers may have been accidentally making GMOs for millennia" (in en). The New Scientist. 2016-03-17. https://www.newscientist.com/article/2079813-farmers-may-have-been-accidentally-making-gmos-for-millennia/. 
  34. ↑ "Recurrent Domestication by Lepidoptera of Genes from Their Parasites Mediated by Bracoviruses". PLOS Genetics 11 (9): e1005470. September 2015. doi:10.1371/journal.pgen.1005470. PMID 26379286. 
  35. ↑ "Genes from Chagas parasite can transfer to humans and be passed on to children" (in en). National Geographic. 2010-02-14. http://phenomena.nationalgeographic.com/2010/02/14/genes-from-chagas-parasite-can-transfer-to-humans-and-be-passed-on-to-children/. 
  36. ↑ "Bacteria-human somatic cell lateral gene transfer is enriched in cancer samples". PLOS Computational Biology 9 (6): e1003107. 2013. doi:10.1371/journal.pcbi.1003107. PMID 23840181. Bibcode: 2013PLSCB...9E3107R. 
  37. ↑ "Horizontal gene transfer in plants". Journal of Experimental Botany 58 (1): 1–9. 2007. doi:10.1093/jxb/erl148. PMID 17030541. http://www.sdsc.edu/~shindyal/ejc121304.pdf. 
  38. ↑ 38.0 38.1 Gogarten, Peter (2000). "Horizontal Gene Transfer: A New Paradigm for Biology". Esalen Center for Theory and Research Conference. http://www.esalenctr.org/display/confpage.cfm?confid=10&pageid=105&pgtype=1. Retrieved 2007-03-18. 
  39. ↑ Kenneth Todar. "Bacterial Resistance to Antibiotics". The Microbial World: Lectures in Microbiology, Department of Bacteriology, University of Wisconsin-Madison. http://textbookofbacteriology.net/themicrobialworld/bactresanti.html. 
  40. ↑ Stanley Maloy (July 15, 2002). "Horizontal Gene Transfer". San Diego State University. http://www.sci.sdsu.edu/~smaloy/MicrobialGenetics/topics/genetic-exchange/exchange/exchange.html. 
  41. ↑ 41.0 41.1 41.2 41.3 41.4 Stearns, S. C., & Hoekstra, R. F. (2005). Evolution: An introduction (2nd ed.). Oxford, NY: Oxford Univ. Press. pp. 38-40.
  42. ↑ "Horizontal Gene Transfer in Eukaryotes: Fungi-to-Plant and Plant-to-Plant Transfers of Organellar DNA". Genomics of Chloroplasts and Mitochondria. Advances in Photosynthesis and Respiration. 35. Springer Science+Business Media B.V.. 2012. pp. 223–235. doi:10.1007/978-94-007-2920-9_10. ISBN 978-94-007-2919-3. 
  43. ↑ "Virus-like particles speed bacterial evolution". Nature. 2010. doi:10.1038/news.2010.507. 
  44. ↑ 44.0 44.1 44.2 44.3 44.4 44.5 44.6 "Promiscuous DNA: horizontal transfer of transposable elements and why it matters for eukaryotic evolution". Trends in Ecology & Evolution 25 (9): 537–46. September 2010. doi:10.1016/j.tree.2010.06.001. PMID 20591532. 
  45. ↑ 45.0 45.1 "Horizontal transfer of transposons between and within crustaceans and insects". Mobile DNA 5 (1): 4. January 2014. doi:10.1186/1759-8753-5-4. PMID 24472097. 
  46. ↑ Aubin E, Llauro C, Garrigue J, Mirouze M, Panaud O, El Baidouri M (2023) Genome-wide analysis of horizontal transfer in non-model wild species from a natural ecosystem reveals new insights into genetic exchange in plants. PLoS Genet 19(10): e1010964. https://doi.org/10.1371/journal.pgen.1010964
  47. ↑ 47.0 47.1 47.2 "Widespread and frequent horizontal transfers of transposable elements in plants". Genome Research 24 (5): 831–8. May 2014. doi:10.1101/gr.164400.113. PMID 24518071. 
  48. ↑ 48.0 48.1 48.2 "Jumping the fine LINE between species: horizontal transfer of transposable elements in animals catalyses genome evolution". BioEssays 35 (12): 1071–82. December 2013. doi:10.1002/bies.201300072. PMID 24003001. 
  49. ↑ Aubin E, Llauro C, Garrigue J, Mirouze M, Panaud O, El Baidouri M (2023) Genome-wide analysis of horizontal transfer in non-model wild species from a natural ecosystem reveals new insights into genetic exchange in plants. PLoS Genet 19(10): e1010964. https://doi.org/10.1371/journal.pgen.1010964
  50. ↑ 50.0 50.1 "Horizontal transposon transfer in eukarya: detection, bias, and perspectives". Genome Biology and Evolution 4 (8): 689–99. 2012. doi:10.1093/gbe/evs055. PMID 22798449. 
  51. ↑ "The virophage as a unique parasite of the giant mimivirus". Nature 455 (7209): 100–4. September 2008. doi:10.1038/nature07218. PMID 18690211. Bibcode: 2008Natur.455..100L. 
  52. ↑ "'Virophage' suggests viruses are alive". Nature 454 (7205): 677. August 2008. doi:10.1038/454677a. PMID 18685665. Bibcode: 2008Natur.454..677P. 
  53. ↑ Barlow M (2009). "What Antimicrobial Resistance Has Taught Us About Horizontal Gene Transfer". Horizontal Gene Transfer. Methods in Molecular Biology. 532. pp. 397–411. doi:10.1007/978-1-60327-853-9_23. ISBN 978-1-60327-852-2. 
  54. ↑ "The changing epidemiology of resistance". The Journal of Antimicrobial Chemotherapy 64 (Suppl 1): i3-10. September 2009. doi:10.1093/jac/dkp256. PMID 19675017. 
  55. ↑ Horizontal Gene Transfer in Microorganisms. Caister Academic Press. 2012. ISBN 978-1-908230-10-2. 
  56. ↑ "Characterization of a Shiga toxin-encoding temperate bacteriophage of Shigella sonnei". Infection and Immunity 69 (12): 7588–95. December 2001. doi:10.1128/IAI.69.12.7588-7595.2001. PMID 11705937. 
  57. ↑ "Integrative and Conjugative Elements (ICEs): What They Do and How They Work". Annual Review of Genetics 42 (1): 577–601. November 2015. doi:10.1146/annurev-genet-112414-055018. PMID 26473380. 
  58. ↑ "The interplay of restriction-modification systems with mobile genetic elements and their prokaryotic hosts". Nucleic Acids Research 49 (16): 10618–10631. September 2014. doi:10.1093/nar/gku734. PMID 25120263. 
  59. ↑ "Identification and characterization of the immunity repressor (ImmR) that controls the mobile genetic element ICE Bs1 of Bacillus subtilis". PLOS Genet 64 (6): 1515–1528. June 2007. doi:10.1111/j.1365-2958.2007.05748.x. PMID 17511812. 
  60. ↑ Gross, H., & Loper, J. E. (2009). Genomics of secondary metabolite production by Pseudomonas spp. Natural product reports, 26(11), 1408-1446.
  61. ↑ "DNA uptake during bacterial transformation". Nature Reviews. Microbiology 2 (3): 241–9. March 2004. doi:10.1038/nrmicro844. PMID 15083159. 
  62. ↑ 62.0 62.1 "Natural genetic transformation: prevalence, mechanisms and function". Research in Microbiology 158 (10): 767–78. December 2007. doi:10.1016/j.resmic.2007.09.004. PMID 17997281. 
  63. ↑ "Who's competent and when: regulation of natural genetic competence in bacteria". Trends in Genetics 12 (4): 150–5. April 1996. doi:10.1016/0168-9525(96)10014-7. PMID 8901420. 
  64. ↑ "Adaptive value of sex in microbial pathogens". Infection, Genetics and Evolution 8 (3): 267–85. May 2008. doi:10.1016/j.meegid.2008.01.002. PMID 18295550. http://www.hummingbirds.arizona.edu/Faculty/Michod/Downloads/IGE%20review%20sex.pdf. 
  65. ↑ "Novel "Superspreader" Bacteriophages Promote Horizontal Gene Transfer by Transformation". mBio 8 (1): e02115-16. January 2017. doi:10.1128/mBio.02115-16. PMID 28096488. 
  66. ↑ 66.0 66.1 "Distributive conjugal transfer in mycobacteria generates progeny with meiotic-like genome-wide mosaicism, allowing mapping of a mating identity locus". PLOS Biology 11 (7): e1001602. July 2013. doi:10.1371/journal.pbio.1001602. PMID 23874149. 
  67. ↑ "Distributive Conjugal Transfer: New Insights into Horizontal Gene Transfer and Genetic Exchange in Mycobacteria". Microbiology Spectrum 2 (1): 61–79. 2014. doi:10.1128/microbiolspec.MGM2-0022-2013. PMID 25505644. 
  68. ↑ "Hundreds of novel composite genes and chimeric genes with bacterial origins contributed to haloarchaeal evolution". Genome Biology 19 (1): 75. June 2018. doi:10.1186/s13059-018-1454-9. PMID 29880023. 
  69. ↑ "Hikarchaeia demonstrate an intermediate stage in the methanogen-to-halophile transition". Nature Communications 11 (1): 5490. October 2020. doi:10.1038/s41467-020-19200-2. PMID 33127909. Bibcode: 2020NatCo..11.5490M. 
  70. ↑ 70.0 70.1 70.2 "UV-inducible cellular aggregation of the hyperthermophilic archaeon Sulfolobus solfataricus is mediated by pili formation". Molecular Microbiology 70 (4): 938–52. November 2008. doi:10.1111/j.1365-2958.2008.06459.x. PMID 18990182. https://pure.rug.nl/ws/files/56956856/UV_inducible_cellular_aggregation_of_the_hyperthermophilic_archaeon_Sulfolobus_solfataricus_is_mediated_by_pili_formation.pdf. 
  71. ↑ "Swapping genes to survive - a new role for archaeal type IV pili". Molecular Microbiology 82 (4): 789–91. November 2011. doi:10.1111/j.1365-2958.2011.07860.x. PMID 21992544. 
  72. ↑ 72.0 72.1 72.2 72.3 "UV-inducible DNA exchange in hyperthermophilic archaea mediated by type IV pili". Molecular Microbiology 82 (4): 807–17. November 2011. doi:10.1111/j.1365-2958.2011.07861.x. PMID 21999488. https://pure.rug.nl/ws/files/6771142/2011MolMicrobiolAjon.pdf. 
  73. ↑ "Reactions to UV damage in the model archaeon Sulfolobus solfataricus". Biochemical Society Transactions 37 (Pt 1): 36–41. February 2009. doi:10.1042/BST0370036. PMID 19143598. 
  74. ↑ "Exchange of genetic markers at extremely high temperatures in the archaeon Sulfolobus acidocaldarius". Journal of Bacteriology 178 (11): 3207–11. June 1996. doi:10.1128/jb.178.11.3207-3211.1996. PMID 8655500. 
  75. ↑ "Genetic responses of the thermophilic archaeon Sulfolobus acidocaldarius to short-wavelength UV light". Journal of Bacteriology 179 (18): 5693–8. September 1997. doi:10.1128/jb.179.18.5693-5698.1997. PMID 9294423. 
  76. ↑ "Biological effects of DNA damage in the hyperthermophilic archaeon Sulfolobus acidocaldarius". FEMS Microbiology Letters 208 (1): 29–34. February 2002. doi:10.1016/s0378-1097(01)00575-4. PMID 11934490. 
  77. ↑ 77.0 77.1 "Molecular analysis of the UV-inducible pili operon from Sulfolobus acidocaldarius". MicrobiologyOpen 2 (6): 928–37. December 2013. doi:10.1002/mbo3.128. PMID 24106028. 
  78. ↑ "DNA Processing Proteins Involved in the UV-Induced Stress Response of Sulfolobales". Journal of Bacteriology 197 (18): 2941–51. September 2015. doi:10.1128/JB.00344-15. PMID 26148716. 
  79. ↑ "Molecular genetics: Horizontal gene transfer". Stillwater, Oklahoma USA: Oklahoma State University. 2001. http://bioinfosu.okstate.edu/MG/MGW3/MG334.html. 
  80. ↑ "Organellar genes: why do they end up in the nucleus?". Trends in Genetics 16 (7): 315–20. July 2000. doi:10.1016/S0168-9525(00)02053-9. PMID 10858662.  Discusses theories on how mitochondria and chloroplast genes are transferred into the nucleus, and also what steps a gene needs to go through in order to complete this process.
  81. ↑ "Host-to-parasite gene transfer in flowering plants: phylogenetic evidence from Malpighiales". Science 305 (5684): 676–8. July 2004. doi:10.1126/science.1100671. PMID 15256617. Bibcode: 2004Sci...305..676D. 
  82. ↑ "Phylogenetic inference in Rafflesiales: the influence of rate heterogeneity and horizontal gene transfer". BMC Evolutionary Biology 4 (1): 40. October 2004. doi:10.1186/1471-2148-4-40. PMID 15496229. 
  83. ↑ "A fragment of chloroplast DNA was transferred horizontally, probably from non-eudicots, to mitochondrial genome of Phaseolus". Plant Molecular Biology 56 (5): 811–20. November 2004. doi:10.1007/s11103-004-5183-y. PMID 15803417. 
  84. ↑ "Contribution of horizontal gene transfer to the evolution of Saccharomyces cerevisiae". Eukaryotic Cell 4 (6): 1102–15. June 2005. doi:10.1128/EC.4.6.1102-1115.2005. PMID 15947202. 
  85. ↑ "Agrobacterium T-DNAs". Frontiers in Plant Science 8: 2015. 2017. doi:10.3389/fpls.2017.02015. PMID 29225610. 
  86. ↑ "Bacterial gene helps coffee beetle get its fix". Nature. 2012. doi:10.1038/nature.2012.10116. 
  87. ↑ "Adaptive horizontal transfer of a bacterial gene to an invasive insect pest of coffee". Proceedings of the National Academy of Sciences of the United States of America 109 (11): 4197–202. March 2012. doi:10.1073/pnas.1121190109. PMID 22371593. Bibcode: 2012PNAS..109.4197A. 
  88. ↑ "Bacterial contribution to genesis of the novel germ line determinant oskar". eLife 24 (9): e45539. Feb 2020. doi:10.7554/eLife.45539. PMID 32091394. 
  89. ↑ Traci Watson (15 November 2012). "Bdelloids Surviving on Borrowed DNA". Science/AAAS News. https://www.science.org/content/article/bdelloids-surviving-borrowed-dna. 
  90. ↑ "No evidence for extensive horizontal gene transfer in the genome of the tardigrade Hypsibius dujardini". Proceedings of the National Academy of Sciences of the United States of America 113 (18): 5053–8. May 2016. doi:10.1073/pnas.1600338113. PMID 27035985. Bibcode: 2016PNAS..113.5053K. 
  91. ↑ "Expression of multiple horizontally acquired genes is a hallmark of both vertebrate and invertebrate genomes". Genome Biology 16 (1): 50. March 2015. doi:10.1186/s13059-015-0607-3. PMID 25785303. 
  92. ↑ "Horizontal Gene Transfer a Hallmark of Animal Genomes?". 2015-03-12. http://www.the-scientist.com/?articles.view/articleNo/42420/title/Horizontal-Gene-Transfer-a-Hallmark-of-Animal-Genomes-/. 
  93. ↑ "Features of a novel protein, rusticalin, from the ascidian Styela rustica reveal ancestral horizontal gene transfer event". Mobile DNA 10 (1): 4. 2019-01-19. doi:10.1186/s13100-019-0146-7. PMID 30675192. 
  94. ↑ "Functional eukaryotic nuclear localization signals are widespread in terminal proteins of bacteriophages". Proceedings of the National Academy of Sciences of the United States of America 109 (45): 18482–7. November 2012. doi:10.1073/pnas.1216635109. PMID 23091024. Bibcode: 2012PNAS..10918482R. 
  95. ↑ "Genome fragment of Wolbachia endosymbiont transferred to X chromosome of host insect". Proceedings of the National Academy of Sciences of the United States of America 99 (22): 14280–5. October 2002. doi:10.1073/pnas.222228199. PMID 12386340. Bibcode: 2002PNAS...9914280K. 
  96. ↑ "Widespread lateral gene transfer from intracellular bacteria to multicellular eukaryotes". Science 317 (5845): 1753–6. September 2007. doi:10.1126/science.1142490. PMID 17761848. Bibcode: 2007Sci...317.1753H. 
  97. ↑ Sloan, D. B., Nakabachi, A., Richards, S., Qu, J., Murali, S. C., Gibbs, R. A., & Moran, N. A. (2014). Parallel histories of horizontal gene transfer facilitated extreme reduction of endosymbiont genomes in sap-feeding insects. Molecular biology and evolution, 31(4), 857-871.
  98. ↑ "Horizontal gene transfer by the parasitic plant Striga hermonthica". Science 328 (5982): 1128. May 2010. doi:10.1126/science.1187145. PMID 20508124. Bibcode: 2010Sci...328.1128Y. 
  99. ↑ Carl Zimmer (April 17, 2014). "Plants That Practice Genetic Engineering". New York Times. https://www.nytimes.com/2014/04/17/science/plants-that-practice-genetic-engineering.html. 
  100. ↑ "FISH labeling reveals a horizontally transferred algal (Vaucheria litorea) nuclear gene on a sea slug (Elysia chlorotica) chromosome". The Biological Bulletin 227 (3): 300–12. December 2014. doi:10.1086/BBLv227n3p300. PMID 25572217. 
  101. ↑ "Why It Is Time to Look Beyond Algal Genes in Photosynthetic Slugs". Genome Biology and Evolution 7 (9): 2602–7. August 2015. doi:10.1093/gbe/evv173. PMID 26319575. 
  102. ↑ "Genome analysis of Elysia chlorotica Egg DNA provides no evidence for horizontal gene transfer into the germ line of this Kleptoplastic Mollusc". Molecular Biology and Evolution 30 (8): 1843–52. August 2013. doi:10.1093/molbev/mst084. PMID 23645554. 
  103. ↑ "Whitefly hijacks a plant detoxification gene that neutralizes plant toxins". Cell 184 (7): 1693–1705.e17. April 2021. doi:10.1016/j.cell.2021.02.014. PMID 33770502. 
  104. ↑ Jaramillo, V. D. A., Vargas, W. A., Sukno, S. A., & Thon, M. R. (2013). New insights into the evolution and structure of Colletotrichum plant-like subtilisins (CPLSs). Communicative & Integrative Biology, 6(6), e59078.
  105. ↑ 105.0 105.1 Nikolaidis, N., Doran, N., & Cosgrove, D. J. (2014). Plant expansins in bacteria and fungi: evolution by horizontal gene transfer and independent domain fusion. Molecular biology and evolution, 31(2), 376-386.
  106. ↑ 106.0 106.1 "Lateral transfer of genes from fungi underlies carotenoid production in aphids". Science 328 (5978): 624–7. April 2010. doi:10.1126/science.1187113. PMID 20431015. Bibcode: 2010Sci...328..624M. 
  107. ↑ "Evolution. A fungal past to insect color". Science 328 (5978): 574–5. April 2010. doi:10.1126/science.1190417. PMID 20431000. Bibcode: 2010Sci...328..574F. 
  108. ↑ "Genes and evolutionary fates of the amanitin biosynthesis pathway in poisonous mushrooms". Proceedings of the National Academy of Sciences of the United States of America 119 (20): e2201113119. May 2022. doi:10.1073/pnas.2201113119. PMID 35533275. Bibcode: 2022PNAS..11901113L. 
  109. ↑ "DNA Jumps Between Animal Species. No One Knows How Often." (in en). 2021-06-09. https://www.quantamagazine.org/dna-jumps-between-animal-species-no-one-knows-how-often-20210609/. 
  110. ↑ "Evidence for a natural gene transfer from the ponyfish to its bioluminescent bacterial symbiont Photobacter leiognathi. The close relationship between bacteriocuprein and the copper-zinc superoxide dismutase of teleost fishes". The Journal of Biological Chemistry 256 (12): 6080–6089. June 1981. doi:10.1016/S0021-9258(19)69131-3. PMID 6787049. 
  111. ↑ Bar D (16 February 2011). "Evidence of Massive Horizontal Gene Transfer Between Humans and Plasmodium vivax". Nature Precedings. doi:10.1038/npre.2011.5690.1. http://precedings.nature.com/documents/5690/version/1/. 
  112. ↑ "Human beings' ancestors have routinely stolen genes from other species". The Economist. 14 March 2015. https://www.economist.com/news/science-and-technology/21646197-human-beings-ancestors-have-routinely-stolen-genes-other-species-genetically?fsrc=scn/gp/wl/pe/geneticallymodifiedpeople. 
  113. ↑ "Microbial genes in the human genome: lateral transfer or gene loss?". Science 292 (5523): 1903–6. June 2001. doi:10.1126/science.1061036. PMID 11358996. Bibcode: 2001Sci...292.1903S. 
  114. ↑ "Microbiological effects of sublethal levels of antibiotics". Nature Reviews. Microbiology 12 (7): 465–478. July 2014. doi:10.1038/nrmicro3270. PMID 24861036. 
  115. ↑ 115.0 115.1 115.2 115.3 115.4 "Non-antibiotic pharmaceuticals promote the transmission of multidrug resistance plasmids through intra- and intergenera conjugation". The ISME Journal 15 (9): 2493–2508. September 2021. doi:10.1038/s41396-021-00945-7. PMID 33692486. Bibcode: 2021ISMEJ..15.2493W. 
  116. ↑ 116.0 116.1 116.2 116.3 116.4 116.5 116.6 "Organic compounds stimulate horizontal transfer of antibiotic resistance genes in mixed wastewater treatment systems". Chemosphere 184: 53–61. October 2017. doi:10.1016/j.chemosphere.2017.05.149. PMID 28578196. Bibcode: 2017Chmsp.184...53J. 
  117. ↑ 117.0 117.1 117.2 117.3 117.4 117.5 117.6 117.7 "Phenolic compounds promote the horizontal transfer of antibiotic resistance genes in activated sludge". The Science of the Total Environment 800: 149549. December 2021. doi:10.1016/j.scitotenv.2021.149549. PMID 34392203. Bibcode: 2021ScTEn.800n9549M. 
  118. ↑ 118.0 118.1 118.2 118.3 118.4 118.5 "Sub-inhibitory concentrations of heavy metals facilitate the horizontal transfer of plasmid-mediated antibiotic resistance genes in water environment". Environmental Pollution 237: 74–82. June 2018. doi:10.1016/j.envpol.2018.01.032. PMID 29477117. 
  119. ↑ "Molecular reconstruction of Sleeping Beauty, a Tc1-like transposon from fish, and its transposition in human cells". Cell 91 (4): 501–510. November 1997. doi:10.1016/S0092-8674(00)80436-5. PMID 9390559. 
  120. ↑ "The Tc1/Mariner Transposon Family". Transposable Elements. Current Topics in Microbiology and Immunology. 204. 1996. pp. 125–143. doi:10.1007/978-3-642-79795-8_6. ISBN 978-3-642-79797-2. 
  121. ↑ "Sleeping Beauty, a wide host-range transposon vector for genetic transformation in vertebrates". Journal of Molecular Biology 302 (1): 93–102. September 2000. doi:10.1006/jmbi.2000.4047. PMID 10964563. 
  122. ↑ "Transgene expression and silencing in a tick cell line: A model system for functional tick genomics". Insect Biochemistry and Molecular Biology 38 (10): 963–968. October 2008. doi:10.1016/j.ibmb.2008.07.008. PMID 18722527. 
  123. ↑ Graham Lawton Why Darwin was wrong about the tree of life New Scientist Magazine issue 2692 21 January 2009 Accessed February 2009
  124. ↑ "Genomic analysis of Hyphomonas neptunium contradicts 16S rRNA gene-based phylogenetic analysis: implications for the taxonomy of the orders 'Rhodobacterales' and Caulobacterales". International Journal of Systematic and Evolutionary Microbiology 55 (Pt 3): 1021–1026. May 2005. doi:10.1099/ijs.0.63510-0. PMID 15879228. 
  125. ↑ "Cladogenesis, coalescence and the evolution of the three domains of life". Trends in Genetics 20 (4): 182–7. April 2004. doi:10.1016/j.tig.2004.02.004. PMID 15041172. 
  126. ↑ 126.0 126.1 126.2 "Uprooting the tree of life". Scientific American 282 (2): 90–5. February 2000. doi:10.1038/scientificamerican0200-90. PMID 10710791. Bibcode: 2000SciAm.282b..90D. 
  127. ↑ "A new biology for a new century". Microbiology and Molecular Biology Reviews 68 (2): 173–86. June 2004. doi:10.1128/MMBR.68.2.173-186.2004. PMID 15187180. 
  128. ↑ "A formal test of the theory of universal common ancestry". Nature 465 (7295): 219–22. May 2010. doi:10.1038/nature09014. PMID 20463738. Bibcode: 2010Natur.465..219T. 
  129. ↑ 129.0 129.1 Harris, Hugh M. B.; Hill, Colin (2021). "A Place for Viruses on the Tree of Life". Frontiers in Microbiology 11. doi:10.3389/fmicb.2020.604048. ISSN 1664-302X. PMID 33519747. 
  130. ↑ "Ancient Gene Transfer as a Tool in Phylogenetic Reconstruction". Horizontal Gene Transfer. Methods in Molecular Biology. 532. Humana Press. 2009. pp. 127–39. doi:10.1007/978-1-60327-853-9_7. ISBN 9781603278522. 
  131. ↑ "Gene transfers can date the tree of life" (in En). Nature Ecology & Evolution 2 (5): 904–909. May 2018. doi:10.1038/s41559-018-0525-3. PMID 29610471. Bibcode: 2018NatEE...2..904D. 
  132. ↑ "Horizontal gene transfer constrains the timing of methanogen evolution" (in En). Nature Ecology & Evolution 2 (5): 897–903. May 2018. doi:10.1038/s41559-018-0513-7. PMID 29610466. Bibcode: 2018NatEE...2..897W. 
  133. ↑ "The chromosomal organization of horizontal gene transfer in bacteria". Nature Communications 8 (1): 841. October 2017. doi:10.1038/s41467-017-00808-w. PMID 29018197. Bibcode: 2017NatCo...8..841O. 
  134. ↑ "Prokaryotic photosynthesis and phototrophy illuminated". Trends in Microbiology 14 (11): 488–96. November 2006. doi:10.1016/j.tim.2006.09.001. PMID 16997562. 
  135. ↑ "Evidence for natural horizontal transfer of tetO gene between Campylobacter jejuni strains in chickens". Journal of Applied Microbiology 97 (1): 134–40. 2004. doi:10.1111/j.1365-2672.2004.02306.x. PMID 15186450. 
  136. ↑ Darkened Forests, Ferns Stole Gene From an Unlikely Source — and Then From Each Other by Jennifer Frazer (May 6, 2014). Scientific American.
  137. ↑ "The origin and evolution of phototropins". Frontiers in Plant Science 6: 637. 2015. doi:10.3389/fpls.2015.00637. PMID 26322073. 
  138. ↑ "A gene horizontally transferred from bacteria protects arthropods from host plant cyanide poisoning". eLife 3: e02365. April 2014. doi:10.7554/eLife.02365. PMID 24843024. 
  139. ↑ "Gonorrhea has picked up human DNA (and that's just the beginning)" (in en). National Geographic. 2011-02-16. http://phenomena.nationalgeographic.com/2011/02/16/gonorrhea-has-picked-up-human-dna-and-thats-just-the-beginning/. 

Further reading

External links

  • Citizendium:Horizontal gene transfer
    Citizendium:Horizontal gene transfer in prokaryotes
    Citizendium:Horizontal gene transfer in plants
    Citizendium:Horizontal gene transfer (History)



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