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Encyclopedia > Horizontal gene transfer

Horizontal gene transfer (HGT), also Lateral gene transfer (LGT), is any process in which an organism transfers genetic material to another cell that is not its offspring. By contrast, vertical transfer occurs when an organism receives genetic material from its ancestor, e.g. its parent or a species from which it evolved. Most thinking in genetics has focussed on the more prevalent vertical transfer, but there is a recent awareness that horizontal gene transfer is a significant phenomenon. Artificial horizontal gene transfer is a form of genetic engineering. For a non-technical introduction to the topic, please see Introduction to genetics. ... An iconic image of genetic engineering; this autoluminograph from 1986 of a glowing transgenic tobacco plant bearing the luciferase, illustrating the possibilities of genetic engineering. ...


As Jain, Rivera and Lake (1999) put it: "Increasingly, studies of genes and genomes are indicating that considerable horizontal transfer has occurred between prokaryotes."[1] Prokaryotes (from Old Greek pro- before + karyon nut or kernel, referring to the cell nucleus, + suffix -otos, pl. ...


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."[2] A microorganism or microbe is an organism that is so small that it is microscopic (invisible to the naked eye). ... Kingdoms Animalia - Animals Fungi Plantae - Plants Protista A eukaryote (IPA: ) is an organism with a complex cell or cells, in which the genetic material is organized into a membrane-bound nucleus or nuclei. ... Typical phyla Chromista Heterokontophyta Haptophyta Cryptophyta (cryptomonads) Alveolata Dinoflagellata Apicomplexa Ciliophora (ciliates) Excavata Euglenozoa Percolozoa Metamonada Rhizaria Radiolaria Foraminifera Cercozoa Archaeplastida (in part) Rhodophyta (red algae) Glaucophyta (basal archaeplastids) Amoebozoa Choanozoa Many others; classification varies Protists (IPA: ) are a diverse group of organisms, comprising those eukaryotes that are not animals...


There is some evidence that even higher plants and animals have been affected. Dr Mae-Wan Ho, a noted scientist and critic of genetic engineering, writes: "While horizontal gene transfer is well-known among bacteria, it is only within the past 10 years that its occurrence has become recognized among higher plants and animals. The scope for horizontal gene transfer is essentially the entire biosphere, with bacteria and viruses serving both as intermediaries for gene trafficking and as reservoirs for gene multiplication and recombination (the process of making new combinations of genetic material)."[3] But Richardson and Palmer (2007) are more cautious: "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."[4] Please wikify (format) this article as suggested in the Guide to layout and the Manual of Style. ... An iconic image of genetic engineering; this autoluminograph from 1986 of a glowing transgenic tobacco plant bearing the luciferase, illustrating the possibilities of genetic engineering. ... A microorganism or microbe is an organism that is so small that it is microscopic (invisible to the naked eye). ... Multicellular organisms are those organisms containing more than one cell, and having differentiated cells that perform specialized functions. ...


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 "A New Paradigm for Biology".[5] Horizontal gene transfer (HGT), also Lateral gene transfer (LGT) is any process in which an organism transfers genetic material (i. ...


It should also be noted that the process is emphasised by Dr Mae-Wan Ho as an important factor in "The Hidden Hazards of Genetic Engineering", as it may allow dangerous transgenic DNA (which is optimised for transfer) to spread from species to species.[3] The structure of part of a DNA double helix. ...

Contents

Prokaryotes

Horizontal gene transfer is common among bacteria, even very distantly-related ones. This process is thought to be a significant cause of increased drug resistance; when one bacterial cell acquires resistance, it can quickly transfer the resistance genes to many species. Enteric bacteria appear to exchange genetic material with each other within the gut in which they live. There are three common mechanisms for horizontal gene transfer: Phyla/Divisions Actinobacteria Aquificae Bacteroidetes/Chlorobi Chlamydiae/Verrucomicrobia Chloroflexi Chrysiogenetes Cyanobacteria Deferribacteres Deinococcus-Thermus Dictyoglomi Fibrobacteres/Acidobacteria Firmicutes Fusobacteria Gemmatimonadetes Nitrospirae Omnibacteria Planctomycetes Proteobacteria Spirochaetes Thermodesulfobacteria Thermomicrobia Thermotogae Bacteria (singular, bacterium) are a major group of living organisms. ... Organisms are said to be drug-resistant when they are no longer affected by drugs that are meant to neutralize them. ... For the Physics term GUT, please refer to Grand unification theory The gastrointestinal or digestive tract, also referred to as the GI tract or the alimentary canal or the gut, is the system of organs within multicellular animals which takes in food, digests it to extract energy and nutrients, and...

  • Transformation, the genetic alteration of a cell resulting from the introduction, uptake and expression of foreign genetic material (DNA or RNA). This process is relatively common in bacteria, but less common in eukaryotes. Transformation is often used 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 bacterial virus (a bacteriophage, commonly called a phage).
  • Bacterial conjugation, a process in which a living bacterial cell transfers genetic material through cell-to-cell contact.

Transformation is the genetic alteration of a cell resulting from the introduction, uptake and expression of foreign genetic material (DNA or RNA). ... Drawing of the structure of cork as it appeared under the microscope to Robert Hooke from Micrographia which is the origin of the word cell. Cells in culture, stained for keratin (red) and DNA (green). ... Gene expression (also protein expression or often simply expression) is the process by which a genes information is converted into the structures and functions of a cell. ... The structure of part of a DNA double helix. ... Ribonucleic acid (RNA) is a nucleic acid polymer consisting of nucleotide monomers. ... Kingdoms Animalia - Animals Fungi Plantae - Plants Protista A eukaryote (IPA: ) is an organism with a complex cell or cells, in which the genetic material is organized into a membrane-bound nucleus or nuclei. ... Molecular biology is the study of biology at a molecular level. ... The structure of insulin Biotechnology is technology based on biology, especially when used in agriculture, food science, and medicine. ... Transduction is the process by which bacterial DNA is moved from one bacterium to another by a virus. ... This article or section does not cite its references or sources. ... Bacterial conjugation is the transfer of genetic material between bacteria through cell-to-cell contact. ...

Eukaryotes

Analysis of DNA sequences suggests that horizontal gene transfer has also occurred within eukaryotes, from their chloroplast and mitochondrial genome to their nuclear genome. As stated in the endosymbiotic theory, chloroplasts and mitochondria probably originated as bacterial endosymbionts of a progenitor to the eukaryotic cell. Horizontal transfer of genes from bacteria to some fungi, especially the yeast Saccharomyces cerevisiae has been well documented. There is also recent evidence that the adzuki bean beetle has somehow acquired genetic material from its (non-beneficial) endosymbiont Wolbachia; however this claim is disputed and the evidence is not conclusive. part of a DNA sequence A DNA sequence (sometimes genetic sequence) is a succession of letters representing the primary structure of a real or hypothetical DNA molecule or strand, The possible letters are A, C, G, and T, representing the four nucleotide subunits of a DNA strand (adenine, cytosine, guanine... Kingdoms Animalia - Animals Fungi Plantae - Plants Protista A eukaryote (IPA: ) is an organism with a complex cell or cells, in which the genetic material is organized into a membrane-bound nucleus or nuclei. ... The endosymbiotic theory, now generally accepted by biologists, concerns the origins of mitochondria and plastids (e. ... An endosymbiont is any organism that lives within the body or cells of another organism, i. ... Divisions Chytridiomycota Zygomycota Ascomycota Basidiomycota The Fungi (singular: fungus) are a large group of organisms ranked as a kingdom within the Domain Eukaryota. ... Binomial name Saccharomyces cerevisiae Meyen ex E.C. Hansen Saccharomyces cerevisiae is a species of budding yeast. ... Wolbachia is a type of bacteria that infects arthropod species, including a high proportion of all insects. ...


"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."[6] For other meanings of this term, see gene (disambiguation). ... In biology, a species is one of the basic units of biodiversity. ... A phylogeny (or phylogenesis) is the origin and evolution of a set of organisms, usually of a species. ...


Evolutionary theory

Horizontal gene transfer is a potential confounding factor in inferring phylogenetic trees based on the sequence of one gene. 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 have substantially diverged. 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. This article contains information that has not been verified and thus might not be reliable. ... It has been suggested that Evolutionary tree be merged into this article or section. ... In mathematics, a sequence is a list of objects (or events) arranged in a linear fashion, such that the order of the members is well defined and significant. ... For other meanings of this term, see gene (disambiguation). ... It has been suggested that Evolutionary tree be merged into this article or section. ...


For example, the most common gene to be used for constructing phylogenetic relationships in prokaryotes is the 16s rRNA 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, validity of 16s rRNA-constructed phylogenetic trees must be reevaluated. Prokaryotes (from Old Greek pro- before + karyon nut or kernel, referring to the cell nucleus, + suffix -otos, pl. ... A non-coding RNA (ncRNA) is any RNA molecule that functions without being translated into a protein. ...


Biologist 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."[7]


"Using single genes as phylogenetic markers, it is difficult to trace organismal phylogeny in the presence of HGT [horizontal gene transfer]. Combining the simple coalescence model of cladogenesis with rare HGT [horizontal gene transfer] events suggest there was no single last 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."[8] For other meanings of this term, see gene (disambiguation). ... In biology, phylogenetics (Greek: phylon = tribe, race and genetikos = relative to birth, from genesis = birth) is the study of evolutionary relatedness among various groups of organisms (e. ... Coalescence is the process by which two or more droplets (or bubbles) merge during contact to form a single daughter droplet (or bubble). ... Cladogenesis is an evolutionary splitting event in which each branch and its smaller branches is a clade; an evolutionary mechanism and a process of adaptive evolution that leads to the development of a greater variety of animals or plants. ... Last universal ancestor (LUA), the hypothetical latest living organism from which all currently living organisms descend. ... For other uses, see Life (disambiguation), Lives (disambiguation) or Living (disambiguation), Living Things (disambiguation). ... In chemistry, a molecule is an aggregate of two or more atoms in a definite arrangement held together by chemical bonds [1] [2] [3] [4] [5]. Chemical substances are not infinitely divisible into smaller fractions of the same substance: a molecule is generally considered the smallest particle of a pure...


Uprooting the Tree of Life by W. Ford Doolittle (Scientific American, February 2000, pp 72-77) contains a discussion of the Last Universal Common Ancestor, and the problems that arose with respect to that concept when one considers horizontal gene transfer. The article covers a wide area - the endosymbiont hypothesis for eukaryotes, the use of small subunit ribosomal RNA (SSU rRNA) as a measure of evolutionary distances (this was the field Carl Woese worked in when formulating the first modern "tree of life", and his research results with SSU rRNA led him to propose the Archaea as a third domain of life) and other relevant topics. Indeed, it was while examining the new three-domain view of life that horizontal gene transfer arose as a complicating issue: Archaeoglobus fulgidus is cited in the article (p.76) as being 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 actually of bacterial origin.[9] W. Ford Doolittle Dr. W. Ford Doolittle (born 1942 in Urbana, Illinois) is a biochemist. ... Scientific American is a popular-science magazine, published (first weekly and later monthly) since August 28, 1845, making it the oldest continuously published magazine in the United States. ... An endosymbiont is any organism that lives within the body or cells of another organism, i. ... Kingdoms Animalia - Animals Fungi Plantae - Plants Protista A eukaryote (IPA: ) is an organism with a complex cell or cells, in which the genetic material is organized into a membrane-bound nucleus or nuclei. ... Ribonucleic acid (RNA) is a nucleic acid polymer consisting of nucleotide monomers. ... Carl Richard Woese (born July 15, 1928) is an American microbiologist famous for defining the Archaea (a new domain or kingdom of life) in 1976 by phylogenetic analysis of 16S ribosomal RNA, a technique pioneered by Woese and which is now standard practice. ... Phyla / Classes Phylum Crenarchaeota Phylum Euryarchaeota     Halobacteria     Methanobacteria     Methanococci     Methanopyri     Archaeoglobi     Thermoplasmata     Thermococci Phylum Korarchaeota Phylum Nanoarchaeota Archaea (; from Greek αρχαία, ancient ones; singular Archaeum, Archaean, or Archaeon), also called Archaebacteria (), is a major division of living organisms. ... For other uses, see Life (disambiguation), Lives (disambiguation) or Living (disambiguation), Living Things (disambiguation). ... A phylogeny (or phylogenesis) is the origin and evolution of a set of organisms, usually of a species. ... Ribbon diagram of the enzyme TIM, surrounded by the space-filling model of the protein. ... HMG-CoA reductase HMG-CoA reductase (or 3-hydroxy-3-methyl-glutaryl-CoA reductase or HMGR) is the first enzyme (EC 1. ...


Again on p.76, the article continues with:

"The weight of evidence still supports the likelihood that mitochondria in eukaryotes derived from alpha-proteobacterial cells and that chloroplasts came from ingested cyanobacteria, but it is no longer safe to assume that those were the only lateral gene transfers that occurred after the first eukaryotes arose. Only in later, multicellular eukaryotes do we know of definite restrictions on horizontal gene exchange, such as the advent of separated (and protected) germ cells."[9]

The article continues with: In cell biology, a mitochondrion is an organelle found in the cells of most eukaryotes. ... Kingdoms Animalia - Animals Fungi Plantae - Plants Protista A eukaryote (IPA: ) is an organism with a complex cell or cells, in which the genetic material is organized into a membrane-bound nucleus or nuclei. ... Chloroplasts are organelles found in plant cells and eukaryotic algae that conduct photosynthesis. ... Orders The taxonomy of the Cyanobacteria is currently under revision. ... A germ cell is a kind of cell that is part of the germline, and is involved in the reproduction of organisms. ...

"If there had never been any lateral gene transfer, all these individual gene trees would have the same topology (the same branching order), and the ancestral genes at the root of each tree would have all been present in the last universal common ancestor, a single ancient cell. But extensive transfer means that neither is the case: gene trees will differ (although many will have regions of similar topology) and there would never have been a single cell that could be called the last universal common ancestor.[9]
"As Woese has written, 'the ancestor cannot have been a particular organism, a single organismal lineage. It was communal, a loosely knit, diverse conglomeration of primitive cells that evolved as a unit, and it eventually developed to a stage where it broke into several distinct communities, which in their turn became the three primary lines of descent (bacteria, archaea and eukaryotes)' In other words, early cells, each having relatively few genes, differed in many ways. By swapping genes freely, they shared various of their talents with their contemporaries. Eventually this collection of eclectic and changeable cells coalesced into the three basic domains known today. These domains become recognisable because much (though by no means all) of the gene transfer that occurs these days goes on within domains."[9]

Phyla Actinobacteria Aquificae Chlamydiae Bacteroidetes/Chlorobi Chloroflexi Chrysiogenetes Cyanobacteria Deferribacteres Deinococcus-Thermus Dictyoglomi Fibrobacteres/Acidobacteria Firmicutes Fusobacteria Gemmatimonadetes Lentisphaerae Nitrospirae Planctomycetes Proteobacteria Spirochaetes Thermodesulfobacteria Thermomicrobia Thermotogae Verrucomicrobia Bacteria (singular: bacterium) are unicellular microorganisms. ... Phyla / Classes Phylum Crenarchaeota Phylum Euryarchaeota     Halobacteria     Methanobacteria     Methanococci     Methanopyri     Archaeoglobi     Thermoplasmata     Thermococci Phylum Korarchaeota Phylum Nanoarchaeota Archaea (; from Greek αρχαία, ancient ones; singular Archaeum, Archaean, or Archaeon), also called Archaebacteria (), is a major division of living organisms. ... Kingdoms Animalia - Animals Fungi Plantae - Plants Protista A eukaryote (IPA: ) is an organism with a complex cell or cells, in which the genetic material is organized into a membrane-bound nucleus or nuclei. ... For other meanings of this term, see gene (disambiguation). ...

See also

Endogenous retroviruses are retroviruses thought to be derived from ancient infections of germ cells in humans, mammals and other vertebrates; as such their proviruses are passed on to the next generation and as such now remain in the genome. ... Germline is a word used in biology and genetics. ... Dividing HeLa cells as seen by electron microscopy for other meanings, see also the disambiguation page Hela A HeLa cell (also Hela or hela cell) is an immortal cell line used in medical research. ... An integron is a gene capture system found in some bacteria. ... A provirus is a retrovirus that has integrated itself into the DNA of a host cell. ... Retrotransposons are genetic elements than can amplify themselves in a genome and are ubiquitous components of the DNA of many eukaryotic organisms. ... The term rhizome has been used by Carl Jung as a metaphor, and by Gilles Deleuze as a concept, and refers to the botanical rhizome. ...

Sources and notes

  1. ^ PNAS Jain, Rivera and Lake (1999)
  2. ^ BMC Evolutionary Biology Bapteste et al. (2005)
  3. ^ a b sfsu.edu Dr Mae-Wan Ho
  4. ^ oxfordjournals.org Richardson and Palmer (2007)
  5. ^ esalenctr.org Peter Gogarten
  6. ^ okstate.edu
  7. ^ Biologist Gogarten at esalenctr.org
  8. ^ Cladogenesis Paper
  9. ^ a b c d Uprooting the Tree of Life by W. Ford Doolittle (Scientific American, February 2000, pp 72-77)
  • Steven L. Salzberg, Owen White, Jeremy Peterson, and Jonathan A. Eisen (2001) "Microbial Genes in the Human Genome: Lateral Transfer or Gene Loss?" Science 292, 1903-1906. [1] (Free full article) This article points out that one dramatic claim of horizontal gene transfer - in which a distinguished group of scientists claimed that bacteria transferred their DNA directly into the human lineage - was simply wrong.
  • Woese, Carl (2002) "On the evolution of cells", PNAS, 99(13) 8742-8747. [2] (Free full article) This article seeks to shift the emphasis in early phylogenic adaptation from vertical to horizontal gene transfer.
  • Hall C, Brachat S, Dietrich FS. "Contribution of Horizontal Gene Transfer to the Evolution of Saccharomyces cerevisiae." Eukaryot Cell 2005 Jun 4(6):1102-15. [3] The article argues that horizontal transfer of bacterial DNA to Saccharomyces cerevisiae has occurred.
  • Natsuko Kondo, Naruo Nikoh, Nobuyuki Ijichi, Masakazu Shimada and Takema Fukatsu (2002) "Genome fragment of Wolbachia endosymbiont transferred to X chromosome of host insect", Proceedings of the National Academy of Sciences of the USA, 99 (22): 14280-14285". [4] (Free full article) This article argues that Wolbachia DNA is in the azuki bean beetle genome (a species of bean weevil
  • Snel B, Bork P, Huynen MA (1999) "Genome phylogeny based on gene content", Nature Genetics, 21(1) 66-67. [5]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 [6]
  • Doolitte, W.Ford (2000) Uprooting the Tree of Life (Scientific American, February 2000, pp 72-77)

Please wikify (format) this article as suggested in the Guide to layout and the Manual of Style. ... W. Ford Doolittle Dr. W. Ford Doolittle (born 1942 in Urbana, Illinois) is a biochemist. ... Scientific American is a popular-science magazine, published (first weekly and later monthly) since August 28, 1845, making it the oldest continuously published magazine in the United States. ... In biology, phylogenetics (Greek: phylon = tribe, race and genetikos = relative to birth, from genesis = birth) is the study of evolutionary relatedness among various groups of organisms (e. ... Wolbachia is a type of bacteria that infects arthropod species, including a high proportion of all insects. ... Genera about 1,350 species The bean weevils or seed beetles are a family Bruchidae (Latreille 1802) of beetles. ...

Further reading

  • Bioinformatics Vol. 22 no. 21 2006, pages 2604–2611 for a technique to decrease the impact of HGT events on maximum likelihood cladistical analyses.
  • Horizontal Gene Transfer - A New Paradigm for Biology
  • Horizontal Gene Transfer (page 334 of Molecular Genetics by Ulrich Melcher)
  • Report on horizontal gene transfer by Mae-Wan Ho, March 22, 1999
  • Recent Evidence Confirms Risks of Horizontal Gene Transfer
  • Horizontal Gene Transfer at sciences.sdsu.edu
  • Horizontal gene transfer among genomes: The complexity hypothesis Vol. 96, Issue 7, 3801-3806, March 30, 1999 of The National Academy of Sciences
  • 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.'"
  • Retrotransfer or gene capture: a feature of conjugative plasmids, with ecological and evolutionary significance
  • Results of research into horizontal gene transfer Can transgenes from genetically modified plants be absorbed by micro-organisms and spread in this way?

  Results from FactBites:
 
BioMed Central | Abstract | Using the nucleotide substitution rate matrix to detect horizontal gene transfer (380 words)
Because transferred genes perform many medically important functions, such as conferring antibiotic resistance, improved detection of horizontally transferred genes from sequence data would be an important advance.
First, we introduce a new class of methods for detecting HGT based on the changes in nucleotide substitution rates that occur when a gene is transferred to a new organism.
These novel indicators of horizontal transfer will be widely useful in detecting HGT events linked to the evolution of important bacterial traits, such as antibiotic resistance and pathogenicity.
Horizontal gene transfer - Wikipedia, the free encyclopedia (702 words)
Horizontal gene transfer is common among bacteria, even very distantly-related ones.
Horizontal gene transfer is a potentially confounding factor in inferring phylogenetic trees based on the sequence of one gene.
For example, the most common gene to be used for constructing phylogenetic relationships in prokaryotes is the 16s rRNA gene, since its sequences tend to be conserved among members with close phylogenetic distances, but variable enough that differences can be measured.
  More results at FactBites »

 
 

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