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Horizontal gene transfer

January 31, 2023

"HGT" redirects here. For other uses, see HGT (disambiguation).
This article is about the natural process. For artificial gene transfer, see Gene delivery.

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] HGT is influencing scientific understanding of higher order evolution while more significantly shifting perspectives on bacterial evolution.[7]

Tree of life showing vertical and horizontal gene transfers

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 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,[24] 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),[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]

HTT has been shown to occur between species and across continents in both plants[46] and animals (Ivancevic et al. 2013), though some TEs have been shown to more successfully colonize the genomes of certain species over others.[47] Both spatial and taxonomic proximity of species has been proposed to favor HTTs in plants and animals.[46] 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.[46] 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.[47]

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

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 article: 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.

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.[49] "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."[50] Horizontal transfer is also seen between geminiviruses and tobacco plants.[51]

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][52] when one bacterial cell acquires resistance, and the resistance genes are transferred to other species.[53][54] 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.[55] 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),[56] and integrons. Still, they are more frequently a chromosomal-encoded barrier to MGE than an MGE-encoded tool for cell infection.[57]

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.[58] Furthermore, it has been linked with the radiation and desiccation resistance of Bacillus pumilus SAFR-032 spores,[59] isolated from spacecraft cleanroom facilities.[60][61][62]

Transposon insertion elements have been reported to increase the fitness of gram-negative E. coli strains through either major transpositions or genome rearrangements, and increasing mutation rates.[63][64] In a study on the effects of long-term exposure of simulated microgravity on non-pathogenic E. coli, the results showed transposon insertions occur at loci, linked to SOS stress response.[65] When the same E. coli strain was exposed to a combination of simulated microgravity and trace (background) levels of (the broad spectrum) antibiotic (chloramphenicol), the results showed transposon-mediated rearrangements (TMRs), disrupting genes involved in bacterial adhesion, and deleting an entire segment of several genes involved with motility and chemotaxis.[66] Both these studies have implications for microbial growth, adaptation to and antibiotic resistance in real time space conditions.

Horizontal gene transfer is particularly active in bacterial genomes around the production of secondary or specialized metabolites.[67][68] This is clearly exhibited within certain groups of bacteria including P. aeruginosa and actinomycetales, an order of Actinomycetota.[69][67] 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.[70][68] Certain areas of genes known as hotspots further increase the likelihood of horizontally transferred secondary metabolite-producing genes.[71] The promiscuity of enzymes is a reoccurring theme in this particular theatre.[68][70]

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.[72][73] 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.[74] 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.[73]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.[75] 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.[76]

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.[77] 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.[77][78]

Archaeal DNA transfer

The archaeon Sulfolobus solfataricus, when UV irradiated, strongly induces the formation of type IV pili which then facilitates cellular aggregation.[79][80] Exposure to chemical agents that cause DNA damage also induces cellular aggregation.[79] 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,[81] 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.[81] Frols et al.[79][82] and Ajon et al.[81] 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.[83] UV exposure induces pili formation and cellular aggregation.[81] 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[84] and by DNA damaging chemicals.[85]

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.[86] Since this system increases the fitness of S. acidocaldarius cells after UV exposure, Wolferen et al.[86][87] 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."[88]

Organelle to nuclear genome

Organelle to organelle

Viruses to plants

  • Plants are capable of receiving genetic information from viruses by horizontal gene transfer.[51]

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.[94]

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.[95][96]
  • 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.[97]

Bacteria to animals

  • Bdelloid rotifers currently hold the 'record' for HGT in animals with ~8% of their genes from bacterial origins.[98] Tardigrades were thought to break the record with 17.5% HGT, but that finding was an artifact of bacterial contamination.[99]
  • 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.[100] The researchers estimated that for some nematodes and Drosophila insects these genes had been acquired relatively recently.[101]
  • A bacteriophage-mediated mechanism transfers genes between prokaryotes and eukaryotes.[102] 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.[103]

Endosymbiont to insects and nematodes

  • The adzuki bean beetle has acquired genetic material from its (non-beneficial) endosymbiont Wolbachia.[104] New examples have recently been reported demonstrating that Wolbachia bacteria represent an important potential source of genetic material in arthropods and filarial nematodes.[105]
  • The psyllid Pachypsylla venusta has acquired genes from its current endosymbiont Carsonella, and from many of its historical endosymbionts, too.[106]

Plant to plant

Plants to animals

Plant to fungus

Main article: Plant-fungus horizontal gene transfer
  • Gene transfer between plants and fungi has been posited for a number of cases, including rice (Oryza sativa).
  • Evidence of gene transfer from plants was documented in the fungus Colletotrichum.[113]
  • Plant expansin genes were transferred to fungi further enabling the fungi to infect plants.[114]

Plant to bacteria

  • Plant expansin genes were transferred to bacteria further enabling the bacteria to infect plants.[115]

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.[118]

Animals to animals

Animals to bacteria

  • The strikingly fish-like copper/zinc superoxide dismutase of Photobacterium leiognathi[120] 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,[122] 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.[123]

Compounds found to promote horizontal gene transfer

Through research into the growing issue of antibiotic resistance[124] certain compounds have been observed to promote horizontal gene transfer.[125][126][127][128] Antibiotics given to bacteria at non-lethal levels have been known to be a cause of antibiotic resistance[128] 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.[125] 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.[125] 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.[125]

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).[126][127] It is a global concern that ARGs have been found in wastewater treatment plants[126] Textile wastewater has been found to contain 3- to 13-fold higher abundance of mobile genetic elements than other samples of wastewater.[126] The cause of this is the organic compounds used for textile dying (o-xylene, ethylbenzene, trioxymethylene, styrene, 2,4-dichloroaniline, and malachite green)[126] raising the frequency of conjugative transfer when bacteria and plasmid (with donor) are introduced in the presence of these molecules.[126] 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.

Other organic pollutants commonly found in wastewater have been the subject of similar experiments.[127] 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.[127] 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.[127] 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).[127] 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[125][126] but their increases is still significant.[127] 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.[127]

Heavy metals have also been found to promote conjugative transfer of antibiotic resistance genes.[128] The paper that led to the discovery of this was done in 2017 during the emerging field of horizontal gene transfer assisting compound research.[128] Metals assist in the spread of antibiotic resistance through both co-resistance as well as cross-resistance mechanisms.[128] 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.[128] 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

See also: Gene therapy
 
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[129] (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.[130] The SB system has been used to introduce genetic sequences into a wide variety of animal genomes.[131][132]

Importance in evolution

See also: Horizontal gene transfer in evolution

Horizontal gene transfer is a potential confounding factor in inferring phylogenetic trees based on the sequence of one gene.[133] 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.[134]

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."[135]

Challenge to the tree of life

Further information: Last universal common ancestor and tree of life (science)

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.[136] 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.[136] 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.[136][137] However, a LUCA can be identified, so horizontal transfers must have been relatively limited.[138]

Phylogenetic information in HGT

It has been remarked that, despite the complications, the detection of horizontal gene transfers brings valuable phylogenetic and dating information.[139]

The potential of HGT to be used for dating phylogenies has recently been confirmed.[140][141]

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.[142]

Genes

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

See also

References

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Further reading

  • Gyles C, Boerlin P (March 2014). "Horizontally transferred genetic elements and their role in pathogenesis of bacterial disease". Veterinary Pathology. 51 (2): 328–40. doi:10.1177/0300985813511131. PMID 24318976. S2CID 206510894.
  • – Papers by Dr Michael Syvanen on Horizontal Gene Transfer
  • Salzberg SL, White O, Peterson J, Eisen JA (June 2001). (PDF). Science. 292 (5523): 1903–6. Bibcode:2001Sci...292.1903S. doi:10.1126/science.1061036. PMID 11358996. S2CID 17016011. Archived from the original (PDF) on 2006-09-01. Retrieved 2005-12-29. About 40 genes were found to be exclusively shared by humans and bacteria and are candidate examples of horizontal transfer from bacteria to vertebrates. Gene loss combined with sample size effects and evolutionary rate variation provide an alternative, more biologically plausible explanation
  • Qi Z, Cui Y, Fang W, Ling L, Chen R (January 2004). "Autosomal similarity revealed by eukaryotic genomic comparison". Journal of Biological Physics. 30 (4): 305–12. doi:10.1007/s10867-004-0996-0. PMC 3456315. PMID 23345874.
  • Woese CR (June 2002). "On the evolution of cells". Proceedings of the National Academy of Sciences of the United States of America. 99 (13): 8742–7. Bibcode:2002PNAS...99.8742W. doi:10.1073/pnas.132266999. PMC 124369. PMID 12077305. This article seeks to shift the emphasis in early phylogenic adaptation from vertical to horizontal gene transfer. He uses the term "Darwinian Threshold" for the time of major transition of evolutionary mechanisms from mostly horizontal to mostly vertical transfer, and the "origin of speciation".
  • Snel B, Bork P, Huynen MA (January 1999). "Genome phylogeny based on gene content". Nature Genetics. 21 (1): 108–10. doi:10.1038/5052. PMID 9916801. S2CID 10296406. This article proposes using the presence or absence of a set of genes to infer phylogenies, in order to avoid confounding factors such as horizontal gene transfer.
  • . Archived from the original on 2005-11-02.
  • Patil PB, Sonti RV (October 2004). "Variation suggestive of horizontal gene transfer at a lipopolysaccharide (lps) biosynthetic locus in Xanthomonas oryzae pv. oryzae, the bacterial leaf blight pathogen of rice". BMC Microbiology. 4 (1): 40. doi:10.1186/1471-2180-4-40. PMC 524487. PMID 15473911.
  • Jin G, Nakhleh L, Snir S, Tuller T (November 2006). "Maximum likelihood of phylogenetic networks". Bioinformatics. 22 (21): 2604–11. doi:10.1093/bioinformatics/btl452. PMID 16928736.
  • Jain R, Rivera MC, Lake JA (March 1999). "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. Bibcode:1999PNAS...96.3801J. doi:10.1073/pnas.96.7.3801. PMC 22375. PMID 10097118.
  • Ochman H, Lawrence JG, Groisman EA (May 2000). "Lateral gene transfer and the nature of bacterial innovation". Nature. 405 (6784): 299–304. Bibcode:2000Natur.405..299O. doi:10.1038/35012500. PMID 10830951. S2CID 85739173.
  • Preston R (July 12, 1999). "The Demon in the Freezer". The New Yorker. pp. 44–61. Smallpox knows how to make a mouse protein. How did smallpox learn that? 'The poxviruses are promiscuous at capturing genes from their hosts,' Esposito said. 'It tells you that smallpox was once inside a mouse or some other small rodent.'
  • Szpirer C, Top E, Couturier M, Mergeay M (December 1999). "Retrotransfer or gene capture: a feature of conjugative plasmids, with ecological and evolutionary significance". Microbiology. 145 (Pt 12): 3321–3329. doi:10.1099/00221287-145-12-3321. PMID 10627031.
  • . GMO Safety: Results of research into horizontal gene transfer. Archived from the original on 2011-07-21.
  • Whitaker JW, McConkey GA, Westhead DR (2009). "The transferome of metabolic genes explored: analysis of the horizontal transfer of enzyme encoding genes in unicellular eukaryotes". Genome Biology. 10 (4): R36. doi:10.1186/gb-2009-10-4-r36. PMC 2688927. PMID 19368726.

External links

 
Scholia has a topic profile for Horizontal gene transfer.

January 31, 2023
horizontal, gene, transfer, redirects, here, other, uses, disambiguation, this, article, about, natural, process, artificial, gene, transfer, gene, delivery, lateral, gene, transfer, movement, genetic, material, between, unicellular, multicellular, organisms, . HGT redirects here For other uses see HGT disambiguation This article is about the natural process For artificial gene transfer see Gene delivery 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 HGT is influencing scientific understanding of higher order evolution while more significantly shifting perspectives on bacterial evolution 7 Tree of life showing vertical and horizontal gene transfers 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 Contents 1 History 2 Mechanisms 2 1 Horizontal transposon transfer 3 Methods of detection 4 Viruses 5 Prokaryotes 5 1 Bacterial transformation 5 2 Bacterial conjugation 5 3 Archaeal DNA transfer 6 Eukaryotes 6 1 Organelle to nuclear genome 6 2 Organelle to organelle 6 3 Viruses to plants 6 4 Bacteria to fungi 6 5 Bacteria to plants 6 6 Bacteria to insects 6 7 Bacteria to animals 6 8 Endosymbiont to insects and nematodes 6 9 Plant to plant 6 10 Plants to animals 6 11 Plant to fungus 6 12 Plant to bacteria 6 13 Fungi to insects 6 14 Fungi to fungi 6 15 Animals to animals 6 16 Animals to bacteria 6 17 Human to protozoan 6 18 Human genome 7 Compounds found to promote horizontal gene transfer 8 Artificial horizontal gene transfer 9 Importance in evolution 9 1 Challenge to the tree of life 9 2 Phylogenetic information in HGT 9 3 The chromosomal organization of horizontal gene transfer 9 4 Genes 10 See also 11 References 12 Further reading 13 External linksHistory EditGriffith 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 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 24 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 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 EditThere are several mechanisms for horizontal gene transfer 5 39 40 Transformation the genetic alteration of a cell resulting from the introduction uptake and expression of foreign genetic material DNA or RNA 41 This process is relatively common in bacteria but less so in eukaryotes 42 Transformation is often used in laboratories to insert novel genes into bacteria for experiments or for industrial or medical applications See also molecular biology and biotechnology Transduction the process in which bacterial DNA is moved from one bacterium to another by a virus a bacteriophage or phage 41 Bacterial conjugation a process that involves the transfer of DNA via a plasmid from a donor cell to a recombinant recipient cell during cell to cell contact 41 Gene transfer agents virus like elements encoded by the host that are found in the alphaproteobacteria order Rhodobacterales 43 Horizontal transposon transfer Edit 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 HTT has been shown to occur between species and across continents in both plants 46 and animals Ivancevic et al 2013 though some TEs have been shown to more successfully colonize the genomes of certain species over others 47 Both spatial and taxonomic proximity of species has been proposed to favor HTTs in plants and animals 46 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 46 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 47 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 47 Moreover transposition activity increases the TE copy number and generates chromosomal rearrangement hotspots 48 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 48 Methods of detection Edit 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 article 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 Viruses EditThe virus called Mimivirus infects amoebae Another virus called Sputnik also infects amoebae but it cannot reproduce unless mimivirus has already infected the same cell 49 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 50 Horizontal transfer is also seen between geminiviruses and tobacco plants 51 Prokaryotes EditHorizontal 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 52 when one bacterial cell acquires resistance and the resistance genes are transferred to other species 53 54 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 55 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 56 and integrons Still they are more frequently a chromosomal encoded barrier to MGE than an MGE encoded tool for cell infection 57 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 58 Furthermore it has been linked with the radiation and desiccation resistance of Bacillus pumilus SAFR 032 spores 59 isolated from spacecraft cleanroom facilities 60 61 62 Transposon insertion elements have been reported to increase the fitness of gram negative E coli strains through either major transpositions or genome rearrangements and increasing mutation rates 63 64 In a study on the effects of long term exposure of simulated microgravity on non pathogenic E coli the results showed transposon insertions occur at loci linked to SOS stress response 65 When the same E coli strain was exposed to a combination of simulated microgravity and trace background levels of the broad spectrum antibiotic chloramphenicol the results showed transposon mediated rearrangements TMRs disrupting genes involved in bacterial adhesion and deleting an entire segment of several genes involved with motility and chemotaxis 66 Both these studies have implications for microbial growth adaptation to and antibiotic resistance in real time space conditions Horizontal gene transfer is particularly active in bacterial genomes around the production of secondary or specialized metabolites 67 68 This is clearly exhibited within certain groups of bacteria including P aeruginosa and actinomycetales an order of Actinomycetota 69 67 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 70 68 Certain areas of genes known as hotspots further increase the likelihood of horizontally transferred secondary metabolite producing genes 71 The promiscuity of enzymes is a reoccurring theme in this particular theatre 68 70 Bacterial transformation Edit 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 72 73 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 74 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 73 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 75 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 76 Bacterial conjugation Edit 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 77 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 77 78 Archaeal DNA transfer Edit The archaeon Sulfolobus solfataricus when UV irradiated strongly induces the formation of type IV pili which then facilitates cellular aggregation 79 80 Exposure to chemical agents that cause DNA damage also induces cellular aggregation 79 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 81 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 81 Frols et al 79 82 and Ajon et al 81 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 83 UV exposure induces pili formation and cellular aggregation 81 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 84 and by DNA damaging chemicals 85 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 86 Since this system increases the fitness of S acidocaldarius cells after UV exposure Wolferen et al 86 87 considered that transfer of DNA likely takes place in order to repair UV induced DNA damages by homologous recombination Eukaryotes Edit 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 88 Organelle to nuclear genome Edit 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 89 Organelle to organelle Edit Mitochondrial genes moved to parasites of the Rafflesiaceae plant family from their hosts 90 91 and from chloroplasts of a still unidentified plant to the mitochondria of the bean Phaseolus 92 Viruses to plants Edit Plants are capable of receiving genetic information from viruses by horizontal gene transfer 51 Bacteria to fungi Edit Horizontal transfer occurs from bacteria to some fungi such as the yeast Saccharomyces cerevisiae 93 Bacteria to plants Edit 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 94 Bacteria to insects Edit 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 95 96 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 97 Bacteria to animals Edit Bdelloid rotifers currently hold the record for HGT in animals with 8 of their genes from bacterial origins 98 Tardigrades were thought to break the record with 17 5 HGT but that finding was an artifact of bacterial contamination 99 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 100 The researchers estimated that for some nematodes and Drosophila insects these genes had been acquired relatively recently 101 A bacteriophage mediated mechanism transfers genes between prokaryotes and eukaryotes 102 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 103 Endosymbiont to insects and nematodes Edit The adzuki bean beetle has acquired genetic material from its non beneficial endosymbiont Wolbachia 104 New examples have recently been reported demonstrating that Wolbachia bacteria represent an important potential source of genetic material in arthropods and filarial nematodes 105 The psyllid Pachypsylla venusta has acquired genes from its current endosymbiont Carsonella and from many of its historical endosymbionts too 106 Plant to plant Edit Striga hermonthica a parasitic eudicot has received a gene from sorghum Sorghum bicolor to its nuclear genome 107 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 108 Plants to animals Edit The eastern emerald sea slug Elysia chlorotica has been suggested by fluorescence in situ hybridization FISH analysis to contain photosynthesis supporting genes obtained from an algae Vaucheria litorea in their diet 109 LGT in Sacoglossa is now thought to be an artifact 110 and no trace of LGT was found upon sequencing the genome of Elysia chlorotica 111 The whitefly Bemisia tabaci acquired a plant detoxification gene that neutralizes plant toxins 112 Plant to fungus Edit Main article Plant fungus horizontal gene transfer Gene transfer between plants and fungi has been posited for a number of cases including rice Oryza sativa Evidence of gene transfer from plants was documented in the fungus Colletotrichum 113 Plant expansin genes were transferred to fungi further enabling the fungi to infect plants 114 Plant to bacteria Edit Plant expansin genes were transferred to bacteria further enabling the bacteria to infect plants 115 Fungi to insects Edit Pea aphids Acyrthosiphon pisum contain multiple genes from fungi 116 117 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 116 Fungi to fungi Edit The toxin a amanitin is found in numerous seemingly unrelated genera fungi such as Amanita Lepiota and Galerina Two biosynthetic genes involved in the production of a 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 118 Animals to animals Edit Smelt fish received antifreeze protein AFP gene from herring through a direct horizontal transfer 119 Animals to bacteria Edit The strikingly fish like copper zinc superoxide dismutase of Photobacterium leiognathi 120 is most easily explained in terms of transfer of a gene from an ancestor of its fish host Human to protozoan Edit The malaria pathogen Plasmodium vivax acquired genetic material from humans that might help facilitate its long stay in the body 121 Human genome Edit One study identified approximately 100 of humans approximately 20 000 total genes which likely resulted from horizontal gene transfer 122 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 123 Compounds found to promote horizontal gene transfer EditThrough research into the growing issue of antibiotic resistance 124 certain compounds have been observed to promote horizontal gene transfer 125 126 127 128 Antibiotics given to bacteria at non lethal levels have been known to be a cause of antibiotic resistance 128 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 125 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 125 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 125 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 126 127 It is a global concern that ARGs have been found in wastewater treatment plants 126 Textile wastewater has been found to contain 3 to 13 fold higher abundance of mobile genetic elements than other samples of wastewater 126 The cause of this is the organic compounds used for textile dying o xylene ethylbenzene trioxymethylene styrene 2 4 dichloroaniline and malachite green 126 raising the frequency of conjugative transfer when bacteria and plasmid with donor are introduced in the presence of these molecules 126 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 Other organic pollutants commonly found in wastewater have been the subject of similar experiments 127 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 127 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 127 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 127 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 125 126 but their increases is still significant 127 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 127 Heavy metals have also been found to promote conjugative transfer of antibiotic resistance genes 128 The paper that led to the discovery of this was done in 2017 during the emerging field of horizontal gene transfer assisting compound research 128 Metals assist in the spread of antibiotic resistance through both co resistance as well as cross resistance mechanisms 128 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 128 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 EditSee also Gene therapy 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 129 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 130 The SB system has been used to introduce genetic sequences into a wide variety of animal genomes 131 132 Importance in evolution EditSee also Horizontal gene transfer in evolution Horizontal gene transfer is a potential confounding factor in inferring phylogenetic trees based on the sequence of one gene 133 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 134 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 135 Challenge to the tree of life Edit Further information Last universal common ancestor and tree of life science 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 136 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 136 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 136 137 However a LUCA can be identified so horizontal transfers must have been relatively limited 138 Phylogenetic information in HGT Edit It has been remarked that despite the complications the detection of horizontal gene transfers brings valuable phylogenetic and dating information 139 The potential of HGT to be used for dating phylogenies has recently been confirmed 140 141 The chromosomal organization of horizontal gene transfer Edit 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 142 Genes Edit This list is incomplete you can help by adding missing items August 2008 There is evidence for historical horizontal transfer of the following genes Lycopene cyclase for carotenoid biosynthesis between Chlorobiota and Cyanobacteria 143 TetO gene conferring resistance to tetracycline between Campylobacter jejuni 144 Neochrome a gene in some ferns that enhances their ability to survive in dim light Believed to have been acquired from algae sometime during the Cretaceous 145 146 Transfer of a cysteine synthase from a bacterium into phytophagous mites and Lepidoptera allowing the detoxification of cyanogenic glucosides produced by host plants 147 The LINE1 sequence has transferred from humans to the gonorrhea bacteria 148 See also Edit Evolutionary biology portalAgrobacterium a bacterium well known for its ability to transfer DNA between itself and plants Endogenous retrovirus Genetically modified organism Inferring horizontal gene transfer Integron Mobile genetic elements Phylogenetic network Phylogenetic tree Provirus Reassortment Retrotransposon Symbiogenesis Tree of life biology XenobiologyReferences Edit Ochman H 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horizontally transferred from bacteria protects arthropods from host plant cyanide poisoning eLife 3 e02365 doi 10 7554 eLife 02365 PMC 4011162 PMID 24843024 Yong E 2011 02 16 Gonorrhea has picked up human DNA and that s just the beginning National Geographic Retrieved 2016 07 14 Further reading EditGyles C Boerlin P March 2014 Horizontally transferred genetic elements and their role in pathogenesis of bacterial disease Veterinary Pathology 51 2 328 40 doi 10 1177 0300985813511131 PMID 24318976 S2CID 206510894 Papers by Dr Michael Syvanen on Horizontal Gene Transfer Salzberg SL White O Peterson J Eisen JA June 2001 Microbial genes in the human genome lateral transfer or gene loss PDF Science 292 5523 1903 6 Bibcode 2001Sci 292 1903S doi 10 1126 science 1061036 PMID 11358996 S2CID 17016011 Archived from the original PDF on 2006 09 01 Retrieved 2005 12 29 About 40 genes were found to be exclusively shared by humans and bacteria and are candidate examples of horizontal transfer from bacteria to vertebrates Gene loss combined with sample size effects and evolutionary rate variation provide an alternative more biologically plausible explanation Qi Z Cui Y Fang W Ling L Chen R January 2004 Autosomal similarity revealed by eukaryotic genomic comparison Journal of Biological Physics 30 4 305 12 doi 10 1007 s10867 004 0996 0 PMC 3456315 PMID 23345874 Woese CR June 2002 On the evolution of cells Proceedings of the National Academy of Sciences of the United States of America 99 13 8742 7 Bibcode 2002PNAS 99 8742W doi 10 1073 pnas 132266999 PMC 124369 PMID 12077305 This article seeks to shift the emphasis in early phylogenic adaptation from vertical to horizontal gene transfer He uses the term Darwinian Threshold for the time of major transition of evolutionary mechanisms from mostly horizontal to mostly vertical transfer and the origin of speciation Snel B Bork P Huynen MA January 1999 Genome phylogeny based on gene content Nature Genetics 21 1 108 10 doi 10 1038 5052 PMID 9916801 S2CID 10296406 This article proposes using the presence or absence of a set of genes to infer phylogenies in order to avoid confounding factors such as horizontal gene transfer Webfocus in Nature with free review articles Archived from the original on 2005 11 02 Patil PB Sonti RV October 2004 Variation suggestive of horizontal gene transfer at a lipopolysaccharide lps biosynthetic locus in Xanthomonas oryzae pv oryzae the bacterial leaf blight pathogen of rice BMC Microbiology 4 1 40 doi 10 1186 1471 2180 4 40 PMC 524487 PMID 15473911 Jin G Nakhleh L Snir S Tuller T November 2006 Maximum likelihood of phylogenetic networks Bioinformatics 22 21 2604 11 doi 10 1093 bioinformatics btl452 PMID 16928736 Jain R Rivera MC Lake JA March 1999 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 Bibcode 1999PNAS 96 3801J doi 10 1073 pnas 96 7 3801 PMC 22375 PMID 10097118 Ochman H Lawrence JG Groisman EA May 2000 Lateral gene transfer and the nature of bacterial innovation Nature 405 6784 299 304 Bibcode 2000Natur 405 299O doi 10 1038 35012500 PMID 10830951 S2CID 85739173 Preston R July 12 1999 The Demon in the Freezer The New Yorker pp 44 61 Smallpox knows how to make a mouse protein How did smallpox learn that The poxviruses are promiscuous at capturing genes from their hosts Esposito said It tells you that smallpox was once inside a mouse or some other small rodent Szpirer C Top E Couturier M Mergeay M December 1999 Retrotransfer or gene capture a feature of conjugative plasmids with ecological and evolutionary significance Microbiology 145 Pt 12 3321 3329 doi 10 1099 00221287 145 12 3321 PMID 10627031 Can transgenes from genetically modified plants be absorbed by micro organisms and spread in this way GMO Safety Results of research into horizontal gene transfer Archived from the original on 2011 07 21 Whitaker JW McConkey GA Westhead DR 2009 The transferome of metabolic genes explored analysis of the horizontal transfer of enzyme encoding genes in unicellular eukaryotes Genome Biology 10 4 R36 doi 10 1186 gb 2009 10 4 r36 PMC 2688927 PMID 19368726 External links Edit Scholia has a topic profile for Horizontal gene transfer Citizendium Horizontal gene transfer Citizendium Horizontal gene transfer in prokaryotes Citizendium Horizontal gene transfer in plants Citizendium Horizontal gene transfer History Retrieved from https en wikipedia org w index php title Horizontal gene transfer amp oldid 1136331694, wikipedia, wiki, book, books, library,

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