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horizontal gene transfer
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{{Redirect|HGT}}{{About|the natural process|artificial gene transfer|Gene delivery}}{{short description|A type of nonhereditary genetic change involving swapping of DNA or RNA other than from parent to offspring}}(File:Tree Of Life (with horizontal gene transfer).svg|thumb|Tree of life showing vertical and horizontal gene transfers)Horizontal gene transfer (HGT) or lateral gene transfer (LGT)JOURNAL, Ochman, H., Lawrence, J. G., & Groisman, E. A., Lateral gene transfer and the nature of bacterial innovation, Nature, 405, 6784, 299–304, May 2000, 10.1038/35012500, 10830951, 2000Natur.405..299O, JOURNAL, Dunning Hotopp, J. C., Horizontal gene transfer between bacteria and animals, Trends in Genetics, 27, 4, 157–163, April 2011, 10.1016/j.tig.2011.01.005, 21334091, 3068243, JOURNAL, Robinson, K. M., Sieber, K. B., & Dunning Hotopp, J. C., A review of bacteria-animal lateral gene transfer may inform our understanding of diseases like cancer, PLoS Genet, 9, 10, e1003877, October 2013, 10.1371/journal.pgen.1003877, 24146634, 3798261, 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).JOURNAL, Patrick J. Keeling, Keeling, P. J., & Jeffrey D. Palmer, Palmer, J.D., Horizontal gene transfer in eukaryotic evolution, Nature Reviews Genetics, 9, 8, 605–618, 2008, 10.1038/nrg2386, 18591983, HGT is an important factor in the evolution of many organisms.JOURNAL, Gyles, C., Boerlin, P., Horizontally transferred genetic elements and their role in pathogenesis of bacterial disease, Veterinary Pathology, March 2014, 51, 2, 328–340, 10.1177/0300985813511131, 24318976, JOURNAL, 10.1111/bij.12872, Speciation through the looking-glass, Biological Journal of the Linnean Society, 120, 2, 480–488, 2017, Vaux, Felix, Trewick, Steven A., Morgan-Richards, Mary, Horizontal gene transfer is the primary mechanism for the spread of antibiotic resistance in bacteria,OECD, Safety Assessment of Transgenic Organisms, Volume 4: OECD Consensus Documents, 2010, pp.171-174JOURNAL, Kay E, Vogel TM, Bertolla F, Nalin R, Simonet P, In situ transfer of antibiotic resistance genes from transgenic (transplastomic) tobacco plants to bacteria, Appl. Environ. Microbiol., 68, 7, 3345–51, July 2002, 12089013, 126776, 10.1128/aem.68.7.3345-3351.2002, JOURNAL, Koonin EV, Makarova KS, Aravind L, Horizontal gene transfer in prokaryotes: quantification and classification, Annu. Rev. Microbiol., 55, 709–42, 2001, 11544372, 10.1146/annurev.micro.55.1.709, 1, 4781227, JOURNAL, Nielsen KM, Barriers to horizontal gene transfer by natural transformation in soil bacteria, APMIS, 84, S84, 77–84, 1998, 9850687, 10.1111/j.1600-0463.1998.tb05653.x, and plays an important role in the evolution of bacteria that can degrade novel compounds such as human-created pesticidesJOURNAL, McGowan C, Fulthorpe R, Wright A, Tiedje JM, Evidence for interspecies gene transfer in the evolution of 2,4-dichlorophenoxyacetic acid degraders, Appl. Environ. Microbiol., 64, 10, 4089–92, October 1998, 9758850, 106609,weblink and in the evolution, maintenance, and transmission of virulence.JOURNAL, Keen, E. C., Paradigms of pathogenesis: Targeting the mobile genetic elements of disease, 10.3389/fcimb.2012.00161, Frontiers in Cellular and Infection Microbiology, 2, 161, December 2012, 23248780, 3522046, It often involves temperate bacteriophages and plasmids.JOURNAL, Naik GA, Bhat LN, Chpoade BA, Lynch JM, Transfer of broad-host-range antibiotic resistance plasmids in soil microcosms, Curr. Microbiol., 28, 1994, 209–215, 10.1007/BF01575963, 4, JOURNAL, Varga M, Kuntova L, Pantucek R, Maslanova I, Ruzickova V, Doskar J, Efficient transfer of antibiotic resistance plasmids by transduction within methicillin-resistant Staphylococcus aureus USA300 clone, FEMS Microbiol. Lett., 332, 2012, 146–152, 10.1111/j.1574-6968.2012.02589.x, 2, 22553940, JOURNAL, Varga M, Pantucek R, Ruzickova V, Doskar J, Molecular characterization of a new efficiently transducing bacteriophage identified in meticillin-resistant Staphylococcus aureus, Journal of General Virology, 97, 2016, 258–268, 10.1099/jgv.0.000329, 1, 26537974, Genes responsible for antibiotic resistance in one species of bacteria can be transferred to another species of bacteria through various mechanisms of HGT such as transformation, transduction and conjugation, subsequently arming the antibiotic resistant genes' recipient against antibiotics. The rapid spread of antibiotic resistance genes in this manner is becoming medically challenging to deal with. Ecological factors may also play a role in the LGT of antibiotic resistant genes.JOURNAL, Hiltunen, Teppo, Virta, Marko, Manu Tamminen, Hultman, Jenni, Ruokolainen, Lasse, Cairns, Johannes, 2018-04-19, Ecology determines how low antibiotic concentration impacts community composition and horizontal transfer of resistance genes, Communications Biology, en, 1, 1, 35, 10.1038/s42003-018-0041-7, 30271921, 6123812, 2399-3642, It is also postulated that HGT promotes the maintenance of a universal life biochemistry and, subsequently, the universality of the genetic code.JOURNAL, Kubyshkin, V., Acevedo-Rocha, C. G., Budisa, N., 2017, On universal coding events in protein biogenesis, Biosystems, 164, 16–25, 10.1016/j.biosystems.2017.10.004, 29030023, Most thinking in genetics has focused upon vertical transfer, but the importance of horizontal gene transfer among single-cell organisms is beginning to be acknowledged.WEB,weblink Horizontal gene transfer in microbes much more frequent than previously thought, Lin Edwards, October 4, 2010, PhysOrg.com, 2012-01-06, JOURNAL,weblink To Share and Share Alike: Bacteria swap genes with their neighbors more frequently than researchers have realized, Carrie Arnold, April 18, 2011, Scientific American, 2012-01-06, 10.1038/scientificamerican0411-30, Gene delivery can be seen as an artificial horizontal gene transfer, and is a form of genetic engineering.

History

Griffith's experiment, reported in 1928 by Frederick Griffith,JOURNAL, Griffith, Fred., Frederick Griffith, The Significance of Pneumococcal Types, Journal of Hygiene, Cambridge University Press, January 1928, 27, 2, 113–159, 4626734, 20474956, 2167760, 10.1017/S0022172400031879, was the first experiment suggesting that bacteria are capable of transferring genetic information through a process known as transformation.JOURNAL, Lorenz, M. G., Wackernagel, W., Bacterial gene transfer by natural genetic transformation in the environment, Microbiology and Molecular Biology Reviews, Microbiological Reviews, 58, 3, 563–602, 1994-09-01, 7968924, 372978, JOURNAL, Downie, A. W., Pneumococcal transformation — a backward view: Fourth Griffith Memorial Lecture, Microbiology (journal), Journal of General Microbiology,weblink 73, 1, 1–11, 1972, 10.1099/00221287-73-1-1, 4143929, 2011-11-30, 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,JOURNAL, Freeman, Victor J, Studies on the virulence of bacteriophage-infected strains of Corynebacterium Diphtheriae, Journal of Bacteriology, 1951, 675–688, 14850426, 61, 6, 386063, 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),Phillip Marguilies "Epidemics: Deadly diseases throughout history". Rosen, New York. 2005. and giving the first example for the relevance of the lysogenic cycle.André Lwoff (1965). "Interaction among Virus, Cell, and Organism". Nobel Lecture for the Nobel Prize in Physiology or Medicine. 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.JOURNAL, Ochiai K, Yamanaka T, Kimura K, Sawada, O, Inheritance of drug resistance (and its transfer) between Shigella strains and Between Shigella and E. coli strains, Hihon Iji Shimpor, 1861, 34, 1959, Japanese, JOURNAL, Akiba T, Koyama K, Ishiki Y, Kimura S, Fukushima T, On the mechanism of the development of multiple-drug-resistant clones of Shigella, Jpn. J. Microbiol., 4, 219–27, April 1960, 13681921, 10.1111/j.1348-0421.1960.tb00170.x, 2, In the mid-1980s, SyvanenJOURNAL, Syvanen M, Cross-species gene transfer; implications for a new theory of evolution, J. Theor. Biol., 112, 2, 333–43, January 1985, 2984477, 10.1016/S0022-5193(85)80291-5,weblink predicted that lateral gene transfer existed, had biological significance, and was involved in shaping evolutionary history from the beginning of life on Earth.As Jian, Rivera and Lake (1999) put it: "Increasingly, studies of genes and genomes are indicating that considerable horizontal transfer has occurred between prokaryotes"JOURNAL, Jain R, Rivera MC, Lake JA, Horizontal gene transfer among genomes: The complexity hypothesis, Proc. Natl. Acad. Sci. U.S.A., 96, 7, 3801–6, March 1999, 10097118, 22375, 10.1073/pnas.96.7.3801, 1999PNAS...96.3801J, (see also Lake and Rivera, 2007).JOURNAL, Rivera MC, Lake JA, The ring of life provides evidence for a genome fusion origin of eukaryotes, Nature, 431, 7005, 152–5, September 2004, 15356622, 10.1038/nature02848,weblink 2004Natur.431..152R, yes,weblink" title="web.archive.org/web/20070927135534weblink">weblink 2007-09-27, 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."JOURNAL, Bapteste E, Susko E, Leigh J, MacLeod D, Charlebois RL, Doolittle WF, Do orthologous gene phylogenies really support tree-thinking?, BMC Evol. Biol., 5, 33, 2005, 15913459, 1156881, 10.1186/1471-2148-5-33, 1, 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.WEB,weblink Farmers may have been accidentally making GMOs for millennia, Le Page, Michael, 2016-03-17, The New Scientist, English, 2016-07-11, Some Lepidoptera (e.g. monarch butterflies and silkworms) have been genetically modified by horizontal gene transfer from the wasp bracovirus.JOURNAL, Gasmi, Laila, Boulain, Helene, Gauthier, Jeremy, Hua-Van, Aurelie, Musset, Karine, Jakubowska, Agata K., Aury, Jean-Marc, Volkoff, Anne-Nathalie, Huguet, Elisabeth, 2015-09-17, Recurrent Domestication by Lepidoptera of Genes from Their Parasites Mediated by Bracoviruses, PLOS Genet, 11, 9, e1005470, 10.1371/journal.pgen.1005470, 1553-7404, 4574769, 26379286, Bites from the insect Reduviidae (assassin bug) can, via a parasite, infect humans with the trypanosomal Chagas disease, which can insert its DNA into the human genome.WEB,weblink Genes from Chagas parasite can transfer to humans and be passed on to children, Yong, Ed, 2010-02-14, National Geographic, English, 2016-07-13, It has been suggested that lateral gene transfer to humans from bacteria may play a role in cancer.JOURNAL, Riley, DR, Sieber, KB, Robinson, KM, White, JR, Ganesan, A, etal, 2013, Bacteria-Human Somatic Cell Lateral Gene Transfer Is Enriched in Cancer Samples, PLoS Comput Biol, 9, 6, e1003107, 10.1371/journal.pcbi.1003107, 23840181, 2013PLSCB...9E3107R, 3688693, 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."JOURNAL, Richardson, Aaron O., Palmer, Jeffrey D., Jeffrey D. Palmer, 2007, Horizontal Gene Transfer in Plants, Journal of Experimental Botany, 58, 1–9,weblink 10.1093/jxb/erl148, 17030541, 1, yes,weblink" title="web.archive.org/web/20070927135534weblink">weblink 2007-09-27, 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".JOURNAL, Gogarten, Peter, 2000, Horizontal Gene Transfer: A New Paradigm for Biology, Esalen Center for Theory and Research Conference,weblink 2007-03-18,

Mechanisms

There are several mechanisms for horizontal gene transfer:WEB,weblink Bacterial Resistance to Antibiotics, Kenneth Todar, The Microbial World: Lectures in Microbiology, Department of Bacteriology, University of Wisconsin-Madison, January 6, 2012, WEB,weblink Horizontal Gene Transfer, Stanley Maloy, July 15, 2002, San Diego State University, January 6, 2012,
  • Transformation, the genetic alteration of a cell resulting from the introduction, uptake and expression of foreign genetic material (DNA or RNA).Stearns, S. C., & Hoekstra, R. F. (2005). Evolution: An introduction (2nd ed.). Oxford, NY: Oxford Univ. Press. pp. 38-40. This process is relatively common in bacteria, but less so in eukaryotes.R. Bock and V. Knoop (eds.), Genomics of Chloroplasts and Mitochondria, Advances in Photosynthesis and Respiration 35, pp. 223–235 {{doi|10.1007/978-94-007-2920-9_10}}, Springer Science+Business Media B.V. 2012 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).
  • 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.
  • Gene transfer agents, virus-like elements encoded by the host that are found in the alphaproteobacteria order Rhodobacterales.JOURNAL, Maxmen, A., Virus-like particles speed bacterial evolution, Nature, 2010, 10.1038/news.2010.507,

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.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.JOURNAL, Schaack S, Clement G, Cedric F, 2010, Promiscuous DNA: Horizontal Transfer of Transposable Elements and Why It Matters for Eukaryotic Evolution, Trends in Ecology and Evolution, 25, 9, 537–46, 10.1016/j.tree.2010.06.001, 20591532, 2940939, 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.JOURNAL, Dupeyron M et al, 2014, Horizontal Transfer of Transposons between and within Crustaceans and Insects, Mobile DNA, 5, 1, 4, 10.1186/1759-8753-5-4, 24472097, 3922705, 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. 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. Horizontal transfer is thought to play an important role in the TE life cycle.HTT has been shown to occur between species and across continents in both plantsJOURNAL, El Baidouri Moaine, 2014, Widespread and Frequent Horizontal Transfers of Transposable Elements in Plants, Genome Research, 24, 5, 831–838, 10.1101/gr.164400.113, etal, 24518071, 4009612, and animals (Ivancevic et al. 2013), though some TEs have been shown to more successfully colonize the genomes of certain species over others.JOURNAL, Ivancevic A. M., Walsh A. M., Kortschak R. D., Adelson D. L., 2013, Jumping the fine LINE between species: Horizontal transfer of transposable elements in animals catalyses genome evolution, BioEssays, 35, 12, 1071–1082, 10.1002/bies.201300072, 24003001, Both spatial and taxonomic proximity of species has been proposed to favor HTTs in plants and animals. 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. 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. 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. Many proposed vectors include arthropods, viruses, freshwater snails (Ivancevic et al. 2013), endosymbiotic bacteria, and intracellular parasitic bacteria. In some cases, even TEs facilitate transport for other TEs.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. Moreover, transposition activity increases the TE copy number and generates chromosomal rearrangement hotspots.JOURNAL, Wallau, Luz G, Freitas Ortiz M, Elgion Lucio SL, 2012, Horizontal Transposon Transfer in Eukarya: Detection, Bias, and Perspectives, 10.1093/gbe/evs055, 22798449, 3516303, Genome Biology and Evolution, 4, 8, 801–811, 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.

Methods of detection

File:Xenology.svg|thumb|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 xenologxenologHorizontal 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.JOURNAL, La Scola B, Desnues C, Pagnier I, Robert C, Barrassi L, Fournous G, Merchat M, Suzan-Monti M, Forterre P, Koonin E, Raoult D, The virophage as a unique parasite of the giant mimivirus, Nature, 455, 7209, 100–4, September 2008, 18690211, 10.1038/nature07218, 2008Natur.455..100L, "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."JOURNAL, Pearson H, 'Virophage' suggests viruses are alive, Nature, 454, 7205, 677, 2008, 18685665, 10.1038/454677a, 2008Natur.454..677P, Horizontal transfer is also seen between geminiviruses and tobacco plants.JOURNAL, Bejarano E.R., Khashoggi A.M., Witty M., Lichtenstein C.P., 1994, Discovery of ancient recombination between geminiviral DNA and the nuclear genome of Nicotiana sp, 10.1073/pnas.93.2.759, 8570630, Proceedings of the National Academy of Sciences, 93, 2, 759–764, 40128, 1996PNAS...93..759B,

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 resistanceBOOK, Barlow M, Horizontal Gene Transfer, What antimicrobial resistance has taught us about horizontal gene transfer, 532, 397–411, 2009, 19271198, 10.1007/978-1-60327-853-9_23, Methods in Molecular Biology, 978-1-60327-852-2, when one bacterial cell acquires resistance, and the resistance genes are transferred to other species.JOURNAL, Hawkey PM, Jones AM, The changing epidemiology of resistance, Journal of Antimicrobial Chemotherapy, 64, Suppl 1, i3–10, September 2009, 19675017, 10.1093/jac/dkp256, BOOK, Francino, MP (editor), 2012, Horizontal Gene Transfer in Microorganisms, Caister Academic Press, 978-1-908230-10-2, 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. Horizontal gene transfer also plays a role in the spread of virulence factors, such as exotoxins and exoenzymes, amongst bacteria. 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.JOURNAL, Strauch, Eckhard, Lurz, Rudi, Beutin, Lothar, Characterization, December 2001, Shigella sonnei, Infection and Immunity, 69, 12, 7588–7595, 10.1128/IAI.69.12.7588-7595.2001, 11705937, 98851, Strategies to combat certain bacterial infections by targeting these specific virulence factors and mobile genetic elements have been proposed. For example, horizontally transferred genetic elements play important roles in the virulence of E. coli, Salmonella, Streptococcus and Clostridium perfringens.In prokaryotes, restriction-modification systems are known to provide immunity against horizontal gene transfer and in stabilizing mobile genetic elements. Genes encoding restriction modification systems have been reported to move between prokaryotic genomes within mobile genetic elements such as plasmids, prophages, insertion sequences/transposons, integrative conjugative elements (ICEs), and integrons. Still, they are more frequently a chromosomal-encoded barrier to MGEs than an MGE-encoded tool for cell infection.JOURNAL, Oliveira, PH, Touchon, M, Rocha, EPC, The interplay of restriction-modification systems with mobile genetic elements and their prokaryotic hosts, Nucleic Acids Res, 2014, 42, 16, 10618–10631, 10.1093/nar/gku734,weblink 25120263, 4176335,

Bacterial transformation

(File:Transformation HGT in Bacteria.svg|thumb|1: Donor bacteria 2: Bacteria who will receive the gene 3: The red portion represents the gene that will be transferred. Transformation in bacteria in a certain environment.)Natural transformation is a bacterial adaptation for DNA transfer (HGT) that depends on the expression of numerous bacterial genes whose products are responsible for this process.JOURNAL, Chen I, Dubnau D, DNA uptake during bacterial transformation, Nat. Rev. Microbiol., 2, 3, 241–9, 2004, 15083159, 10.1038/nrmicro844, JOURNAL, Johnsborg O, Eldholm V, Håvarstein LS, Natural genetic transformation: prevalence, mechanisms and function, Res. Microbiol., 158, 10, 767–78, 2007, 17997281, 10.1016/j.resmic.2007.09.004, 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.JOURNAL, Solomon JM, Grossman AD, Who's competent and when: regulation of natural genetic competence in bacteria, Trends Genet., 12, 4, 150–5, 1996, 8901420, 10.1016/0168-9525(96)10014-7, 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.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.JOURNAL, Michod RE, Bernstein H, Nedelcu AM, Adaptive value of sex in microbial pathogens, Infect. Genet. Evol., 8, 3, 267–85, May 2008, 18295550, 10.1016/j.meegid.2008.01.002,weblink 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.JOURNAL, Keen, Eric C., Bliskovsky, Valery V., Malagon, Francisco, Baker, James D., Prince, Jeffrey S., Klaus, James S., Adhya, Sankar L., Groisman, Eduardo A., Novel "Superspreader" Bacteriophages Promote Horizontal Gene Transfer by Transformation, mBio, 8, 1, 2017, e02115-16, 2150-7511, 10.1128/mBio.02115-16, 28096488, 5241400,

Bacterial conjugation

(File:Conjugation HGT in Bacteria.svg|thumb|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.JOURNAL, Gray TA, Krywy JA, Harold J, Palumbo MJ, Derbyshire KM, Distributive conjugal transfer in mycobacteria generates progeny with meiotic-like genome-wide mosaicism, allowing mapping of a mating identity locus, PLoS Biol., 11, 7, e1001602, 2013, 23874149, 3706393, 10.1371/journal.pbio.1001602, 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.JOURNAL, Derbyshire KM, Gray TA, Distributive Conjugal Transfer: New Insights into Horizontal Gene Transfer and Genetic Exchange in Mycobacteria, Microbiol Spectr, 2, 1, 61–79, 2014, 25505644, 4259119, 10.1128/microbiolspec.MGM2-0022-2013,

Archaeal DNA transfer

The archaeon Sulfolobus solfataricus, when UV irradiated, strongly induces the formation of type IV pili which then facilitates cellular aggregation.JOURNAL, Fröls S, Ajon M, Wagner M, Teichmann D, Zolghadr B, Folea M, Boekema EJ, Driessen AJ, Schleper C, Albers SV, UV-inducible cellular aggregation of the hyperthermophilic archaeon Sulfolobus solfataricus is mediated by pili formation, Mol. Microbiol., 70, 4, 938–52, 2008, 18990182, 10.1111/j.1365-2958.2008.06459.x, JOURNAL, Allers T, Swapping genes to survive - a new role for archaeal type IV pili, Mol. Microbiol., 82, 4, 789–91, 2011, 21992544, 10.1111/j.1365-2958.2011.07860.x, Exposure to chemical agents that cause DNA damage also induces cellular aggregation. 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,JOURNAL, Ajon M, Fröls S, van Wolferen M, Stoecker K, Teichmann D, Driessen AJ, Grogan DW, Albers SV, Schleper C, UV-inducible DNA exchange in hyperthermophilic archaea mediated by type IV pili, Mol. Microbiol., 82, 4, 807–17, 2011, 21999488, 10.1111/j.1365-2958.2011.07861.x, 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. Frols et al.JOURNAL, Fröls S, White MF, Schleper C, Reactions to UV damage in the model archaeon Sulfolobus solfataricus, Biochem. Soc. Trans., 37, Pt 1, 36–41, 2009, 19143598, 10.1042/BST0370036, and Ajon et al. suggested that UV-inducible DNA transfer is likely an important mechanism for providing increased repair of damaged DNA via homologous recombination. This process can be regarded as a simple form of sexual interaction.Another thermophilic species, Sulfolobus acidocaldarius, is able to undergo HGT. S. acidocaldarius can exchange and recombine chromosomal markers at temperatures up to 84oC.JOURNAL, Grogan DW, Exchange of genetic markers at extremely high temperatures in the archaeon Sulfolobus acidocaldarius, J. Bacteriol., 178, 11, 3207–11, 1996, 8655500, 178072, 10.1128/jb.178.11.3207-3211.1996, UV exposure induces pili formation and cellular aggregation. 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-irradiationJOURNAL, Wood ER, Ghané F, Grogan DW, Genetic responses of the thermophilic archaeon Sulfolobus acidocaldarius to short-wavelength UV light, J. Bacteriol., 179, 18, 5693–8, 1997, 9294423, 179455, 10.1128/jb.179.18.5693-5698.1997, and by DNA damaging chemicals.JOURNAL, Reilly MS, Grogan DW, Biological effects of DNA damage in the hyperthermophilic archaeon Sulfolobus acidocaldarius, FEMS Microbiol. Lett., 208, 1, 29–34, 2002, 11934490, 10.1016/s0378-1097(01)00575-4, 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.JOURNAL, van Wolferen M, Ajon M, Driessen AJ, Albers SV, Molecular analysis of the UV-inducible pili operon from Sulfolobus acidocaldarius, Microbiologyopen, 2, 6, 928–37, 2013, 24106028, 3892339, 10.1002/mbo3.128, Since this system increases the fitness of S. acidocaldarius cells after UV exposure, Wolferen et al.JOURNAL, van Wolferen M, Ma X, Albers SV, DNA Processing Proteins Involved in the UV-Induced Stress Response of Sulfolobales, J. Bacteriol., 197, 18, 2941–51, 2015, 26148716, 4542170, 10.1128/JB.00344-15, 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."Ulrich Melcher (2001) "Molecular genetics: Horizontal gene transfer," Oklahoma State University (Stillwater, Oklahoma USA)

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.JOURNAL, Blanchard JL, Lynch M, Organellar genes: why do they end up in the nucleus?, Trends Genet., 16, 7, 315–20, July 2000, 10858662, 10.1016/S0168-9525(00)02053-9, 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.

Bacteria to fungi

  • Horizontal transfer occurs from bacteria to some fungi, such as the yeast Saccharomyces cerevisiae.JOURNAL, Hall C, Brachat S, Dietrich FS, Contribution of Horizontal Gene Transfer to the Evolution of Saccharomyces cerevisiae, Eukaryotic Cell, 4, 6, 1102–15, June 2005, 15947202, 1151995, 10.1128/EC.4.6.1102-1115.2005,

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.JOURNAL, 10.3389/fpls.2017.02015, 29225610, 5705623, Horizontal Gene Transfer Contributes to Plant Evolution: The Case of Agrobacterium T-DNAs, Frontiers in Plant Science, 8, 2015, 2017, Quispe-Huamanquispe, Dora G., Gheysen, Godelieve, Kreuze, Jan F.,

Endosymbiont to insects and nematodes

  • The adzuki bean beetle has acquired genetic material from its (non-beneficial) endosymbiont Wolbachia.JOURNAL, Kondo N, Nikoh N, Ijichi N, Shimada M, Fukatsu T, Genome fragment of Wolbachia endosymbiont transferred to X chromosome of host insect, Proc. Natl. Acad. Sci. U.S.A., 99, 22, 14280–5, October 2002, 12386340, 137875, 10.1073/pnas.222228199, 2002PNAS...9914280K, New examples have recently been reported demonstrating that Wolbachia bacteria represent an important potential source of genetic material in arthropods and filarial nematodes.JOURNAL, Dunning Hotopp JC, Widespread lateral gene transfer from intracellular bacteria to multicellular eukaryotes, Science, 317, 5845, 1753–6, September 2007, 17761848, 10.1126/science.1142490, vanc, Clark ME, Oliveira DC, 3, Foster, J. M., Fischer, P., Torres, M. C. M., Giebel, J. D., Kumar, N., Ishmael, N., 2007Sci...317.1753H,

Organelle to organelle

  • Mitochondrial genes moved to parasites of the Rafflesiaceae plant family from their hostsJOURNAL, Science, 30 July 2004, 305, 5684, 676–8, 10.1126/science.1100671, Host-to-parasite gene transfer in flowering plants: phylogenetic evidence from Malpighiales, Davis CC, Wurdack KJ, 15256617, 2004Sci...305..676D, JOURNAL, Phylogenetic inference in Rafflesiales: the influence of rate heterogeneity and horizontal gene transfer, Daniel L Nickrent, Daniel Lee Nickrent, Albert Blarer, Yin-Long Qiu, Romina Vidal-Russell, Frank E Anderson, BMC Evolutionary Biology, 2004, 4, 10.1186/1471-2148-4-40, 40, 15496229, 528834, 1, and from chloroplasts of a still-unidentified plant to the mitochondria of the bean Phaseolus.JOURNAL, Magdalena Woloszynska, Tomasz Bocer, Pawel Mackiewicz, Hanna Janska, A fragment of chloroplast DNA was transferred horizontally, probably from non-eudicots, to mitochondrial genome of Phaseolus, Plant Molecular Biology, 56, 5, November 2004, 10.1007/s11103-004-5183-y, 811–20, 15803417,

Plant to plant

  • Striga hermonthica, a parasitic eudicot, has received a gene from sorghum (Sorghum bicolor) to its nuclear genome.JOURNAL, Yoshida, Satoko, Maruyama, Shinichiro, Nozaki, Hisayoshi, Shirasu, Ken, 28 May 2010, Science, 328, 1128, 10.1126/science.1187145, 5982, 20508124, Horizontal gene transfer by the parasitic plant Striga hermonthica, 2010Sci...328.1128Y, 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.NEWS, Plants That Practice Genetic Engineering, April 17, 2014, Carl Zimmer, New York Times,weblink

Fungi to insects

  • Pea aphids (Acyrthosiphon pisum) contain multiple genes from fungi.JOURNAL, Fukatsu T, Evolution. A fungal past to insect color, Science, 328, 5978, 574–5, April 2010, 20431000, 10.1126/science.1190417, 2010Sci...328..574F, 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.JOURNAL, Nancy A. Moran, Tyler Jarvik, 2010, Lateral Transfer of Genes from Fungi Underlies Carotenoid Production in Aphids, Science, 328, 5978, 624–627, 10.1126/science.1187113, 20431015, 2010Sci...328..624M,

Human to protozoan

  • The malaria pathogen Plasmodium vivax acquired genetic material from humans that might help facilitate its long stay in the body.JOURNAL, Bar D, Evidence of Massive Horizontal Gene Transfer Between Humans and Plasmodium vivax, 16 February 2011, Nature Precedings, 10.1038/npre.2011.5690.1,weblink

Bacteria to insects

  • HhMAN1 is a gene in the genome of the coffee borer beetle (Hypothenemus hampei) that resembles bacterial genes, and is thought to be transferred from bacteria in the beetle's gut.JOURNAL, Nature, 2012, 10.1038/nature.2012.10116, Bacterial gene helps coffee beetle get its fix, Lee Phillips, Melissa, JOURNAL, PNAS, Adaptive horizontal transfer of a bacterial gene to an invasive insect pest of coffee, 2012, 10.1073/pnas.1121190109, 109, 11, 4197–4202, 22371593, 3306691, Acuña R, Padilla BE, Flórez-Ramos CP, Rubio JD, Herrera JC, Benavides P, Lee SJ, Yeats TH, Egan AN, Doyle JJ, Rose JK, 2012PNAS..109.4197A,

Viruses to plants

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

Human genome

  • One study identified approximately 100 of humans' approximately 20,000 total genes which likely resulted from horizontal gene transfer,NEWS, 14 March 2015, Human beings' ancestors have routinely stolen genes from other species,weblink The Economist, 17 March 2015, 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 evolutionJOURNAL, Science, 2001, 10.1126/science.1061036, Microbial Genes in the Human Genome: Lateral Transfer or Gene Loss?, Salzberg, S.L., 11358996, 292, 5523, 1903–6, 2001Sci...292.1903S,

Bacteria to animals

  • Bdelloid rotifers currently hold the 'record' for HGT in animals with ~8% of their genes from bacterial origins.WEB,weblink Bdelloids Surviving on Borrowed DNA, Traci Watson, 15 November 2012, Science/AAAS News, Tardigrades were thought to break the record with 17.5% HGT, but that finding was an artifact of bacterial contamination.JOURNAL, Koutsovoulos, Georgios, Kumar, Sujai, Laetsch, Dominik R., Stevens, Lewis, Daub, Jennifer, Conlon, Claire, Maroon, Habib, Thomas, Fran, Aboobaker, Aziz A., Blaxter, Mark, No evidence for extensive horizontal gene transfer in the genome of the tardigradeHypsibius dujardini, Proceedings of the National Academy of Sciences, 2016, 5053–5058, 0027-8424, 10.1073/pnas.1600338113, 113, 18, 27035985, 4983863, 2016PNAS..113.5053K,
  • 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.JOURNAL, 25785303, 10.1186/s13059-015-0607-3, 16, Expression of multiple horizontally acquired genes is a hallmark of both vertebrate and invertebrate genomes, 4358723, 2015, Genome Biol., 50, Crisp A, Boschetti C, Perry M, Tunnacliffe A, Micklem G, The researchers estimated that for some nematodes and Drosophilia insects these genes had been acquired relatively recently.WEB,weblink Horizontal Gene Transfer a Hallmark of Animal Genomes?, Madhusoodanan, Jyoti, 2015-03-12, The Scientist, 2016-07-14,
  • A bacteriophage-mediated mechanism transfers genes between prokaryotes and eukaryotes. Nuclear localization signals in bacteriophage terminal proteins (TP) prime DNA replication and become covalently linked to the viral genome. The role of virus and bacteriophages in HGT in bacteria, suggests that TP-containing genomes could be a vehicle of inter-kingdom genetic information transference all throughout evolution.JOURNAL, Redrejo-Rodríguez, M, Muñoz-Espín, D, Holguera, I, Mencía, M, Salas, M, Functional eukaryotic nuclear localization signals are widespread in terminal proteins of bacteriophages, Proc. Natl. Acad. Sci. U.S.A., 2012, 23091024, 3494942,weblink 10.1073/pnas.1216635109, 109, 45, 18482–7, 2012PNAS..10918482R,

Plants to animals

  • The eastern emerald sea slug Elysia chlorotica has been suggested by FISH analysis to contain photosynthesis-supporting genes obtained from an algae (Vaucheria litorea) in their diet.JOURNAL, Schwartz, Julie A., Curtis, Nicholas E., Pierce, Sidney K., 2014-12-01, FISH Labeling Reveals a Horizontally Transferred Algal (Vaucheria litorea) Nuclear Gene on a Sea Slug (Elysia chlorotica) Chromosome, The Biological Bulletin, 227, 3, 300–312, 10.1086/BBLv227n3p300, 0006-3185, 25572217, LGT in Sacoglossa is now thought to be an artifactJOURNAL, Rauch, Cessa, de Vries, Jan, Rommel, Sophie, Rose, Laura E, Woehle, Christian, Christa, Gregor, Laetz, Elise M, Wägele, Heike, Tielens, Aloysius GM, Nickelsen, Jörg, Schumann, Tobias, Jahns, Peter, Gould, Sven B, Why It Is Time to Look Beyond Algal Genes in Photosynthetic Slugs, Genome Biology and Evolution, 7, 9, 2602–2607, 10.1093/gbe/evv173, 26319575, 4607529, 2015, and no trace of LGT was found upon sequencing the genome of Elysia chlorotica.JOURNAL, Bhattacharya, D, Pelletreau, KN, Price, DC, Sarver, KE, Rumpho, ME, 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, 2013, 30, 8, 1843–1852, 10.1093/molbev/mst084, 23645554, 3708498,

Plant-fungus

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

Artificial horizontal gene transfer

(File:Artificial Bacterial Transformation.svg|thumb|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 systemJOURNAL, Ivics Z., Hackett P.B., Plasterk R.H., Izsvak Z., 1997, Molecular reconstruction of Sleeping Beauty, a Tc1-like transposon from fish, and its transposition in human cells, 10.1016/S0092-8674(00)80436-5, Cell, 91, 4, 501–510, 9390559, (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.JOURNAL, Plasterk RH, The Tc1/mariner transposon family, Curr. Top. Microbiol. Immunol., 204, 125–43, 1996, 8556864, 10.1007/978-3-642-79795-8_6, Current Topics in Microbiology and Immunology, 978-3-642-79797-2, The SB system has been used to introduce genetic sequences into a wide variety of animal genomes.JOURNAL, Izsvak Z., Ivics Z., Plasterk R.H., 2000, Sleeping Beauty, a wide host-range transposon vector for genetic transformation in vertebrates, J. Mol. Biol., 302, 1, 93–102, 10964563, 10.1006/jmbi.2000.4047, JOURNAL, Kurtti TJ, Mattila JT, Herron MJ, etal, Transgene expression and silencing in a tick cell line: A model system for functional tick genomics, Insect Biochem. Mol. Biol., 38, 10, 963–8, October 2008, 18722527, 2581827, 10.1016/j.ibmb.2008.07.008, (See also Gene therapy.)

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.Graham Lawton Why Darwin was wrong about the tree of life New Scientist Magazine issue 2692 21 January 2009 Accessed February 2009 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.Genomic analysis of Hyphomonas neptunium contradicts 16S rRNA gene-based phylogenetic analysis: implications for the taxonomy of the orders 'Rhodobacterales' and CaulobacteraesBiologist 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". 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."JOURNAL, Zhaxybayeva, O., Gogarten, J., 10.1016/j.tig.2004.02.004, Cladogenesis, coalescence and the evolution of the three domains of life, Trends in Genetics, 20, 4, 182–187, 2004, 15041172,

Challenge to the tree of life

{{further|Last universal common ancestor|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.JOURNAL, Doolittle, Ford W., February 2000, Uprooting the Tree of Life, Scientific American, 72–7, 10710791, Ford Doolittle, 10.1038/scientificamerican0200-90, 282, 2, 2000SciAm.282b..90D, 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. 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.JOURNAL, Woese CR, A New Biology for a New Century, Microbiol. Mol. Biol. Rev., 68, 2, 173–86, June 2004, 15187180, 419918, 10.1128/MMBR.68.2.173-186.2004, However, a LUCA can be identified, so horizontal transfers must have been relatively limited.JOURNAL, Theobald, Douglas L., 13 May 2010, Nature, 465, 219–222, 10.1038/nature09014, 7295, 20463738, A formal test of the theory of universal common ancestry, 2010Natur.465..219T,

Phylogenetic information in HGT

On the opposite, it has been remarked that the detection of Horizontal Gene Transfers could bring valuable phylogenetic and dating information.BOOK, Horizontal Gene Transfer, 532, Huang, Jinling, Gogarten, Johann Peter, 2009, Humana Press, 9781603278522, Methods in Molecular Biology, 127–139, en, 10.1007/978-1-60327-853-9_7, 19271182, The potential of HGT to be used for dating phylogenies has recently been confirmed.JOURNAL, Davín, Adrián A., Tannier, Eric, Williams, Tom A., Boussau, Bastien, Daubin, Vincent, Szöllősi, Gergely J., 2018-04-02, Gene transfers can date the tree of life, Nature Ecology & Evolution, 2, 5, 904–909, En, 10.1038/s41559-018-0525-3, 29610471, 5912509, 2397-334X, JOURNAL, Wolfe, Joanna M., Fournier, Gregory P., 2018-04-02, Horizontal gene transfer constrains the timing of methanogen evolution, Nature Ecology & Evolution, 2, 5, 897–903, En, 10.1038/s41559-018-0513-7, 29610466, 2397-334X,

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.JOURNAL, Oliveira, Pedro H., Touchon, Marie, Cury, Jean, Rocha, Eduardo PC, 10.1038/s41467-017-00808-w, 29018197, 5635113, The chromosomal organization of horizontal gene transfer in bacteria, Nature Communications, 8, 841, 1–111, 2017, 2017NatCo...8..841O,

Genes

{{Expand list|date=August 2008}}There is evidence for historical horizontal transfer of the following genes: "MEMBERWIDE">AUTHOR2=N.-U. FRIGAARD, November 2006, Prokaryotic photosynthesis and phototrophy illuminated, Trends Microbiol., 14, 11, 488–96, 10.1016/j.tim.2006.09.001, 16997562,
  • TetO gen conferring resistance to tetracycline, between Campylobacter jejuni.JOURNAL, Avrain L, Vernozy-Rozand C, Kempf I, Evidence for natural horizontal transfer of tetO gene between Campylobacter jejuni strains in chickens, J. Appl. Microbiol., 97, 1, 134–40, 2004, 15186450, 10.1111/j.1365-2672.2004.02306.x,
  • Neochrome, gene in some ferns that enhances their ability to survive in dim light. Believed to have been acquired from algae sometime during the Cretaceous.Darkened Forests, Ferns Stole Gene From an Unlikely Source — and Then From Each Other by Jennifer Frazer (May 6, 2014). Scientific American.JOURNAL, Li, FW, Rothfels, CJ, Melkonian, M, Villarreal, JC, Stevenson, DW, Graham, SW, Wong, GK, Mathews, S, Pryer, KM, The origin and evolution of phototropins., Frontiers in Plant Science, 2015, 6, 637, 10.3389/fpls.2015.00637, 26322073, 4532919,
  • transfer of a cysteine synthase from a bacterium into phytophagous mites and Lepidoptera allowing the detoxification of cyanogenic glucosides produced by host plants.JOURNAL, Wybouw, Nicky, Dermauw, Wannes, Tirry, Luc, Stevens, Christian, Grbić, Miodrag, Feyereisen, René, Leeuwen, Thomas Van, 2014-04-24, A gene horizontally transferred from bacteria protects arthropods from host plant cyanide poisoning, eLife, en, 3, e02365, 10.7554/eLife.02365, 2050-084X, 4011162, 24843024,
  • The LINE1 sequence has transferred from humans to the gonorrhea bacteria.WEB,weblink Gonorrhea has picked up human DNA (and that's just the beginning), Yong, Ed, 2011-02-16, National Geographic, English, 2016-07-14,

See also

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Sources and notes

{{Reflist|2}}

Further reading

{{Scholia|topic}}
  • (:Citizendium:Horizontal gene transfer)
  • (:Citizendium:Horizontal gene transfer in prokaryotes)
  • (:Citizendium:Horizontal gene transfer in plants)
  • (:Citizendium:Horizontal gene transfer (History))
  • JOURNAL, Gyles, C, Boerlin, P, Mar 2014, Horizontally transferred genetic elements and their role in pathogenesis of bacterial disease, Vet Pathol, 51, 2, 328–40, 10.1177/0300985813511131, 24318976,
  • – Papers by Dr Michael Syvanen on Horizontal Gene Transfer
  • JOURNAL, Salzberg SL, White O, Peterson J, Eisen JA, Microbial genes in the human genome: lateral transfer or gene loss?, Science, 292, 5523, 1903–6, June 2001, 11358996, 10.1126/science.1061036,weblink 2001Sci...292.1903S, 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,
  • JOURNAL, Qi, Z, Cui, Y, Fang, W, Ling, L, Chen, R, Autosomal similarity revealed by eukaryotic genomic comparison., Journal of Biological Physics, January 2004, 30, 4, 305–12, 23345874, 10.1007/s10867-004-0996-0, 3456315,
  • JOURNAL, Woese CR, On the evolution of cells, Proc. Natl. Acad. Sci. U.S.A., 99, 13, 8742–7, June 2002, 12077305, 124369, 10.1073/pnas.132266999, 2002PNAS...99.8742W, 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".
  • JOURNAL, Snel B, Bork P, Huynen MA, Genome phylogeny based on gene content, Nat. Genet., 21, 1, 108–10, January 1999, 9916801, 10.1038/5052, 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 weblink
  • JOURNAL, Patil PB, Sonti RV, 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 Microbiol., 4, 40, October 2004, 15473911, 524487, 10.1186/1471-2180-4-40, 1,
  • JOURNAL, Jin G, Nakhleh L, Snir S, Tuller T, Maximum likelihood of phylogenetic networks, Bioinformatics, 22, 21, 2604–11, November 2006, 16928736, 10.1093/bioinformatics/btl452, for a technique to decrease the impact of HGT events on maximum likelihood cladistical analyses.
  • Horizontal Gene Transfer – A New Paradigm for Biology
  • weblink" title="web.archive.org/web/19990220101406weblink">Horizontal Gene Transfer (page 334 of Molecular Genetics by Ulrich Melcher)
  • Horizontal Gene Transfer at sciences.sdsu.edu
  • JOURNAL, Jain R, Rivera MC, Lake JA, Horizontal gene transfer among genomes: The complexity hypothesis, Proc. Natl. Acad. Sci. U.S.A., 96, 7, 3801–6, March 1999, 10097118, 22375, 10.1073/pnas.96.7.3801, 1999PNAS...96.3801J,
  • PDF article on Horizontal Gene Transfer
  • The New Yorker, July 12, 1999, 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.'"
  • JOURNAL, Szpirer C, Top E, Couturier M, Mergeay M, Retrotransfer or gene capture: a feature of conjugative plasmids, with ecological and evolutionary significance, Microbiology, 145, Pt 12, 3321–9, 1 December 1999, 10627031,weblink 10.1099/00221287-145-12-3321,
  • GMO Safety: Results of research into horizontal gene transfer Can transgenes from genetically modified plants be absorbed by micro-organisms and spread in this way?
  • JOURNAL, Whitaker JW, McConkey GA, Westhead DR, The transferome of metabolic genes explored: analysis of the horizontal transfer of enzyme encoding genes in unicellular eukaryotes, Genome Biology, 10, 4, R36, 2009, 19368726, 2688927, 10.1186/gb-2009-10-4-r36,
{{Genetic recombination}}

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