Horizontal gene transfer/Citable Version: Difference between revisions

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<blockquote> <center>The Rhyme of the Ancient Mariner, ''Samuel Taylor Coleridge''
{{subpages}}
:He prayeth well, who loveth well
:Both man and bird and beast.
:He prayeth best, who loveth best
:All things both great and small
</center></blockquote>
Introductory discussions of [[genetics]] of multicellular organisms tend to emphasise '''vertical gene transfer''', that is simple heritability of parental traits by progeny when an organism receives genetic material from its ancestor, e.g. its parents or other ancestral members of the same species.  The possibility of '''horizontal gene transfer (HGT)''', also called  '''lateral gene transfer (LGT)''', which  is any process in which an organism transfers genetic material (i.e. [[DNA]]) to another cell that is not its offspring, is often not mentioned.


The historical concept of a genome as a stable structure that is faithfully inherited from generation to generation has also tended to cause the biological importance of horizontal gene transfer to be overlooked. Although [[Barbara McClintock]] realised in the 1940s the the genome (in maize) was in fact a dynamic structure, her work was not fully appreciated until mobile DNA and horizontal gene transfer in bacteria was thoroughly studied in the 1960s and 70s <ref> Beckwith, J. and Sihavy, T.J. (1992) The Power of Bacterial Genetics: A Literature-based Course. Cold Spring Harbor Laboratory Press. ISBN 0-87969-379-7 </ref>
[[Image:Legionella pneumophila-s.jpg|right|frame|''[[Legionella pneumophila]]'' are [[prokaryote|prokaryotic]] bacteria that can survive and reproduce inside [[phagocytic]] cells such as protists that have eaten them. They are competent in DNA [[transformation]] and occasionally capture genes from their [[eukaryotic]] host cells.]]


* '''A hallmark of horizontal gene transfer''' is the presence of the same gene in distantly related organisms. The frequent discovery of shared DNA sequences such as the ''mariner'' class of [[transposons]], [[insertion sequence]] (IS) DNA, and [[retrovirus]] genes in diverse species, and shared mitochondial genes in diverse flowering plants indicates that [[mobile DNA]] has natural pathways for movement between different species.
'''Horizontal gene transfer''' occurs when an [[organism]] transfers its genetic material to a being ''other'' than one of its own offspring. The actual process of this transfer can be by any mechanism, but because genes are not passing by descent, horizontal gene transfer (abbreviated as HGT) is always very different from [[Biological inheritance|vertical gene transfer]]. In vertical descent, parental traits are inherited by progeny by one of two general methods: either (1) ''sexual reproduction'' in which [[gametes]] form [[zygotes]], a common method in higher animals and plants, or (2) by ''asexual reproduction'', where splitting of cells or an entire organism grows from a fragment, as is usual in [[bacteria]] and [[Fungus|fungi]], but which also happens in some animals and plants. HGT is a much more recently discovered route of passage for genetic material; it is relatively common in [[microorganism]]s, and to a lesser extent in plants. By HGT, genetic material can be shared between organisms without the immediate relatedness of mother cell to daughter cells, or parent organisms to offspring; indeed, by HGT material can pass between organismsthat are not even be of the same [[species]], [[genus]], sub-kingdom or kingdom of life form. HGT (sometimes called ''lateral'' gene transfer) is very much less common than vertical gene transfer, so its detection requires special techniques.


* '''Horizontal movement of genes''' is common among [[bacteria]] and is responsible for '''infectious multiple-antibiotic resistance''' in pathogenic bacteria, a major factor limiting the effectiveness of antibiotics.
==Introduction==
Evidence from [[genomics|genome]] science and [[bioinformatics]] shows that HGT has occurred between diverse biological [[taxa]] that are widely separated in the [[phylogeny|phylogenetic]] [http://www.tolweb.org/tree/ tree of life]. Known HGTs include movement of genetic material between different species of microbes and other microbial taxa such as protists, gene movement between different plant families, between different animals, and between bacteria and plants. [[Image:Cobwebsoflife.jpg|right|frame|HGT — gene exchange between non-related organisms —appears commonplace among bacteria, but contributes just small fragments of genetic information, leaving the traditional tree of life intact. From: [http://biology.plosjournals.org/perlserv/?request=slideshow&type=figure&doi=10.1371/journal.pbio.0030347&id=36052    Comparing Gene Trees and Genome Trees: A Cobweb of Life? PLoS Biol 3:e347]]]


* '''Horizontal gene transfer'''  is also common in diverse groups of unicellular [[protists]], which often contain several genes transfered from both [[prokaryotes]] and other protists <ref> Richards, T. A., Hirt, R. P., Williams, B. A. & Embley, T. M. (2003) Protist 1, 17–32.</ref> <ref>[http://www.jbc.org/cgi/reprint/M304359200v1.pdf Graham H. Coomb Gareth D. Westrop, Pavel Suchan, Gabriela Puzova, Robert P. Hirt, T. Martin Embley, Jeremy C. Mottramc and Sylke Müllerd (2003) The amitochondriate eukaryote ''Trichomonas vaginalis'' contains a divergent thioredoxin-linked peroxiredoxin antioxidant system JBC Papers in Press. Published on November 20, 2003 as Manuscript M304359200]</ref> <ref>[http://www.biomedcentral.com/content/pdf/1471-2148-6-27.pdf Jan O Andersson, Robert P Hirt, Peter G Foster and Andrew J Roger (2006) Evolution of four gene families with patchy phylogenetic distributions: influx of genes into protist genomes BMC Evolutionary Biology 2006, 6:27 doi:10.1186/1471-2148-6-27]</ref>.
Microorganisms appear to be most affected by HGT, but even in microbes only about 2% of core genes are transferred laterally. Because this percentage is so low, the main lineages of microbial evolution can still be treated as 'trees' branched by vertical descent, with HGT included in the scheme only as 'cobwebs' (see figure at right).  


* '''Horizontal gene transfer''' globally occurs on a massive scale among marine microorganisms, and viruses, the most numerous biological entities in the sea, are implicated as a major pathway for inter-species gene movement in the ocean.
Gene transfers between different biological [[Three-domain system|sub-kingdoms]] (domains), such as between [[eukaryote|eukaryotic]] protists and bacteria, or between bacteria and insects are the most phylogenetically extreme cases of HGT. An example is bacterial 'rol' genes from ''Agrobacterium'' species which have been found in tobacco plants (''Nicotiniana'').<ref>de Felipe K ''et al.'' (2005) Evidence for acquisition of Legionella type IV secretion substrates via interdomain horizontal gene transfer. J Bacteriol [http://jb.asm.org/cgi/content/full/187/22/7716?view=long&pmid=16267296 187:7716-26]  PMID 16267296 (Open access)
* Kondo N ''et al.'' (2002) Genome fragment of ''Wolbachia'' endosymbiont transferred to X chromosome of host insect. Proc Natl Acad Sci USA [http://www.pnas.org/cgi/content/full/99/22/14280 99:14280-5]  PMID 12386340 (Open access)
* Intrieri MC, Buiatti M (2001) The horizontal transfer of ''Agrobacterium'' rhizogenes genes and the evolution of the genus ''Nicotiana''. Mol Phylogen Evol 20:100-10 PMID 11421651</ref>


* '''Mechanisims for horizontal gene transfer''' in flowering plants involving parasitic or endophte intermediaries (which are in intimite cell-to-cell contact with their host plants) are now well established. But not all '''the vehicles by which horizontal gene transfer''' are  fully characterised. '''Horizontal gene transfer''' occurs at lower frequencies than routine exchange of a full set of genes as occurs with sexual reproduction within the species, making difficlt to detect directly, but modern techniques of DNA analysis provide much evidence for it from comparative study of genomes. In insects, mites and insect viruses are established as probable vectors for transmission for horizontal gene transfer. Other mechanisms include [[plasmid]] mediated promiscuous mating by bacteria, for instance by''[[Agrobacterium tumefaciens]]'', and carriage of genes by [[viruses]].  
HGT is just one of several processes that can cause rearrangement of genomes during evolution. The possibility of intracellular movement of genes between different parts of an organism's genome (that is, between the [[chromosomes]] of the [[nucleus]], the circular [[mitochondrion]] chromosome, or the circular [[plastid]] ([[chloroplast]]) chromosome) needs to be considered when evaluating HGT between different species.<ref>Timmis JN  ''et al.'' (2004) Endosymbiotic gene transfer: organelle genomes forge eukaryotic chromosomes. Nat Rev Genet 5:123-35  PMID 14735123</ref>


* Bacterial "rol" genes from ''Agrobacterium'' species are present in plants of the tobacco (''Nicotiniana'') genus. <ref>Maria Carmela Intrieri and Marcello Buiatti 2002 The Horizontal Transfer of Agrobacterium rhizogenes Genes and the Evolution of the Genus Nicotiana.  Molecular Phylogenetics and Evolution Volume 20, Issue 1 , July 2001, Pages 100-110</ref>
==Main features of HGT in nature==
* A hallmark of HGT is the presence of the same gene in organisms that are only very distantly related to each other. The frequent discovery of shared DNA sequences such as the ''mariner'' class of [[transposons]], [[insertion sequence]] DNA, [[retrovirus]] genes in diverse species and shared mitochondrial genes in diverse flowering plants indicate that [[mobile DNA]] has natural pathways for movement between species. (The name mariner for a class of related transposons is an allusion to ''The Rime of the Ancient Mariner'', meaning a traveller to distant lands.) Close relatives of ''mariner'' mobile DNA have been identified in organisms as diverse as mites, flatworms, hydras, insects, nematodes, mammals and humans.<ref>Robertson HM (1996) Reconstruction of the ancient ''mariners'' of humans. Nat Genet 12:360-1 PMID 8630486
*[http://etext.virginia.edu/toc/modeng/public/Col2Mar.html ''The Rime of the Ancient Mariner'']Samuel Taylor Coleridge(1772-1834)</ref>  


[[Image:Millet.jpg|right|frame|Millet. From: [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0040035 ''Jumping Genes Cross Plant Species Boundaries.'']Analysis of the genomes of millet and rice revealed evidence for HGT between chromosomes in the nucleus of one plant to chromosomes in the nucleus of a reproductively isolated species]]
* Horizontal movement of genes is common among bacteria, and is a major factor in accelerating the rate of their evolution. HGT is involved in multiple-antibiotic resistance in pathogenic bacteria, and this is a major factor that is limiting the effectiveness of antibiotics. Inter-domain (sub-kingdom) transfer of several genes from eukaryotes to bacteria for instance, has occurred in the 'accidentally pathogenic' bacterium (''Legionella pneumophila'', see illustration) that lives within vacuoles of [[protist]] and mammalian [[macrophage]] cells.<ref>Jain R ''et al.'' (2003) Horizontal gene transfer accelerates genome innovation and evolution. Mol Biol Evol [http://mbe.oxfordjournals.org/cgi/content/full/20/10/1598 20:1598-602]  PMID 12777514 (Open access)
* de Felipe KS ''et al.'' (2005) Evidence for acquisition of ''Legionella'' type IV secretion substrates via interdomain horizontal gene transfer. J Bacteriol[http://jb.asm.org/cgi/content/full/187/22/7716?view=long&pmid=16267296 187:7716-26]  PMID 16267296 (Open access) </ref>
* HGT is documented in diverse unicellular protists, which can contain several genes transferred from both [[prokaryotes]] and other protists.<ref>Andersson JO ''et al.'' (2006) Evolution of four gene families with patchy phylogenetic distributions: influx of genes into protist genomes.[http://www.biomedcentral.com/1471-2148/6/27  BMC Evol Biol]  PMID 16551352 (Open access)
* Loftus B ''et al.'' (2005) The genome of the protist parasite ''Entamoeba histolytica''. Nature 433:865-8  PMID 15729342</ref>
* HGT occurs globally on a massive scale among marine microorganisms. Viruses, which, at total numbers near 10<sup>29</sup> are the most common biological entities in the sea, are a major pathway for gene movement between different species. It has been estimated that, on average, 10<sup>13</sup> virus-mediated gene transfer events occur in the Mediterranean sea each year. [[Endosymbiosis]] with an alga is identified as a route for HGT in marine [[dinoflagellates]], the organisms that cause 'red tides'.<ref>Fuhrman JA (1999) Marine viruses and their biogeochemical and ecological effects. Nature 399:541–8  PMID 10376593
*Yoon HS ''et al.'' (2005) Tertiary endosymbiosis driven genome evolution in dinoflagellate algae. Mol Biol Evol [http://mbe.oxfordjournals.org/cgi/content/full/22/5/1299 22:1299-308]  PMID 15746017 (Open access)</ref>
* Interspecies gene movement by cross-hybridization is common in flowering plants. Mechanisms for HGT in flowering plants between more distant taxa involving parasitic plants such as dodder and endophytes (such as mosses, which are in intimate cell-to-cell contact with their host plants) are also well established (see [[Horizontal gene transfer in plants]]). Plant mitochondria can be unusually active in HGT.
* Not all of the ways in which HGT occurs are fully characterized, but some have been identified. HGT is hard to detect directly, as it is relatively rare within a species, but can be detected by modern DNA analysis which can enable detailed comparison of [[genomics|genome]]s. In insects, mites and viruses are probably vectors for HGT. In certain bacteria, surface appendages called [[Pilus|pili]] have various roles in DNA uptake, DNA secretion and DNA transfer which have been extensively analyzed; HGT in bacteria includes [[plasmid]]-mediated promiscuous mating by bacteria (for instance by the crown-gall bacterium ''Agrobacterium tumefaciens'') and carriage of genes between species by viruses. Direct DNA uptake is another transfer mechanism, as illustrated by ''Legionella'' bacteria, which are naturally competent for DNA uptake.


==Prokaryotes==
==Prokaryotes==
{{stub}}
:''See main article [[Horizontal gene transfer in prokaryotes|HGT in prokaryotes]]''
Horizontal gene transfer is common among [[bacterium|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:
:''The three main mechanisms of HGT in bacteria and archaea discussed here are:''
* '''[[Transformation (genetics)|Transformation]]''', the genetic alteration of a [[cell (biology)|cell]] resulting from the introduction, uptake and [[expression (genetics)|expression]] of foreign genetic material ([[DNA]] or [[RNA]]). This process is relatively common in bacteria, but less common in [[eukaryote]]s.  Transformation is often used to insert novel genes into bacteria for experiments, or for industrial or medical applications.  See also [[molecular biology]] and [[biotechnology]].
:* '''''Bacterial [[Transformation (genetics)|Transformation]]''' or direct uptake of extracellular DNA.''
* '''[[Transduction (genetics)|Transduction]]''', the process in which bacterial DNA is moved from one bacterium to another by a bacterial virus (a bacteriophage, commonly called a [[phage]]).
:* '''''[[Transduction (genetics)|Transduction]]''' of genes by bacterial viruses.''
* '''[[Bacterial conjugation]]''', a process in which a living bacterial cell transfers genetic material through cell-to-cell contact.
:* '''''[[Bacterial conjugation]]''', a gene transfer process carried out by plasmids and conjugative transposons.''


==Eukaryotes==
==Eukaryotes==
: ''See also [[Endosymbiotic theory]]''


[[Junk DNA]] is the most obvious evidence of '''horizontal gene transfer in eukaryotes'''. Such seemingly non-functional repetitive DNA which contitutes a major portion of many genomes of plants and animals. This DNA usually includes multiple copies of various "[[Jumping genes]]" which can proliferate within a genome after they have been transferred from another species. Examples in the human of such horizontally transferred mobile are ''Hsmar1'' and ''Hsmar2'' which are related to the widely studied ''mariner'' transposon. Close relatives ''mariner'' mobile DNA have been discovered in organisms as diverse as mites, flatworms, hydras, insects, nematodes, mammals and humans<ref> Robertson, H. M. (1993) The ''mariner'' transposable element is widespread in insects. Nature, 362: p241-245.</ref> <ref>Robertson, H. M. (1996) Reconstruction of the ancient ''mariners'' of humans. Nature Genetics 12, page 360-361.</ref>.
===Protists===
Analysis of the complete genome sequence of the protist ''Entamoeba histolytica'' indicates 96 cases of relatively recent HGT from prokaryotes. There is also convincing evidence that a bacterial gene for a biosynthetic enzyme has been recruited by the protist ''Trichomonas vaginalis'' from bacteria related to the ancestors of ''Pasteurella'' bacteria. Similar analysis of the protist ''Cryptosporidium parvum'' reveals 24 candidates of HGT from bacteria. These results fit the idea that 'you are what you eat'. That is, in unicellular grazing organisms, foreign genetic material is constantly entering the cell from food organisms, and occasionally some of this material enters the genome.<ref>Loftus B ''et al.'' (2005) The genome of the protist parasite ''Entamoeba histolytica''. Nature 433:865-8  PMID 15729342
* Doolittle WF (1998) You are what you eat: a gene transfer ratchet could account for bacterial genes in eukaryotic nuclear genomes. Trends in Genetics 14:307-11  PMID 9724962</ref>
 
===Fungi===
Comparison of the genome sequences of two fungi, baker's yeast (''Saccharomyces cerevisiae'') and ''Ashbya gossypii'', has shown that ''Saccharomyces'' has received two genes from bacteria by HGT. One of these genes codes for an enzyme that allows baker's yeast to make pyrimidine nucleotide bases anaerobically, and the other allows usage of sulfur from several organic sulfur sources. Other work with yeasts suggests that eight genes from ''Yarrowia lipolytica'', five from ''Kluyveromyces lactis'', and one  from ''Debaryomyces hansenii'' are horizontally transferred.<ref>Dujon B ''et al.'' {2004) Genome evolution in yeasts. Nature 430:35-44  PMID 15229592</ref>
 
===Other eukaryotes===
Analysis of [[DNA sequence]]s suggests that HGT has also occurred within multicellular eukaryotes, by a route that involves transfer of genes from  chloroplast and mitochondrial genomes to the nuclear genomes.<ref>Adams KL Palmer JD (2003) Evolution of mitochondrial gene content: gene loss and transfer to the nucleus. Mol Phylogenet Evol 29:380–95  PMID 14615181</ref> According to the [[endosymbiotic theory]], chloroplasts and mitochondria originated as the bacterial [[endosymbiont]]s of a progenitor to the eukaryotic cell, and endosymbiosis can be considered to be a special case of HGT.


Analysis of [[DNA sequence]]s suggests that horizontal gene transfer has also occurred within [[eukaryote]]s, from their chloroplast and mitochondrial genome to their nuclear genome.  As stated in the [[endosymbiotic theory]], chloroplasts and mitochondria probably originated as bacterial [[endosymbiont]]s of a progenitor to the eukaryotic cell.
===Protists===
Analysis of the complete genome sequence of the protist ''Entamoeba histolytica'' indicates 96 cases of relatively recent horizontal gene transfer from prokaryotes <ref>Loftus B, Anderson I, Davies R, Alsmark UCM, Samuelson J, Amedeo P, Roncaglia P, Berriman M, Hirt RP, Mann BJ, Nozaki T, Suh B, Pop M, Duchene M, Ackers J, Tannich E, Leippe M, Hofer M, Bruchhaus I, Willhoeft U, Bhattacharya A, Chillingworth T, Churcher C, Hance Z, Harris B, Harris D, Jagels K, Moule S, Mungall K, Ormond D, Squares R, Whitehead S, Quail MA, Rabbinowitsch E, Norbertczak H, Price C, Wang Z, Guillen N, Gilchrist C, Stroup SE, Bhattacharya S, Lohia A, Foster PG, Sicheritz-Ponten T, Weber C, Singh U, Mukherjee C, El- Sayed NM, Petri WAJ, Clark CG, Embley TM, Barrell B, Fraser CM, Hall N: The genome of the protist parasite  ''Entamoeba histolytica''. Nature 2005, 433(7028):865-868.</ref>, where as similar analysis of the complete genome sequence of the protist ''Cryptosporidium parvum''  reveal 24 candidates of horizontal gene transfer from bacteria <ref>Huang J, Mullapudi N, Lancto CA, Scott M, Abrahamsen MS, Kissinger JC: Phylogenomic evidence supports past [[endosymbiosis]], intracellular and horizontal gene transfer in Cryptosporidium parvum. Genome Biol 2004, 5(11):R88.</ref>. These results fit the idea that "you are what you eat". That is, with unicellular grazing organisms, foreign genetic material is constantly entering the cell and occasionaly the genome from  food organisms <ref>Doolittle WF.(1998) You are what you eat: a gene transfer ratchet could account for bacterial genes in eukaryotic nuclear genomes.Trends Genet. 1998 Aug;14(8):307-11. </ref>.
===Plants===
===Plants===
:''See [[Horizontal gene transfer in plants]] for''
:''See [[Horizontal gene transfer in plants]] for''
:*''Natural gene transfer between plants that do not cross-pollinate''
:*''Natural gene transfer between plants that do not cross-pollinate''
Line 44: Line 60:
:''See [[Transgenic plant]] for hybridization by cross-pollination and artificial horizontal gene transfer in [[biotechnology]].''  
:''See [[Transgenic plant]] for hybridization by cross-pollination and artificial horizontal gene transfer in [[biotechnology]].''  


Plant genes have also been discovered to be able to move to endophyte fungi that grow on them. Several plant endophyte fungi that grow on taxol producing yew trees have gained ability to make taxol themselves <ref>Shrestha K, Strobel GA, Shrivastava SP, Gewali MB. (2001) Evidence for paclitaxel from three new endophytic fungi of Himalayan yew of Nepal. Planta Med. 2001 Jun;67(4):374-6. </ref>. (Taxol is an anti-cancer drug also called paclitaxel found in yew trees.)
It has also been discovered that plant genes can move to endophyte fungi that grow on them. Several plant endophyte fungi that grow on taxol-producing yew trees have gained the ability to make taxol themselves.<ref>Shrestha K ''et al.'' (2001) Evidence for paclitaxel from three new endophytic fungi of Himalayan yew of Nepal. Planta Med 67:374-6 PMID 11458463</ref> (Taxol, also called paclitaxel, is an anti-cancer drug found in yew trees.)
 
Horizontal transfer of genes from bacteria to some [[fungi]], especially the yeast ''[[Saccharomyces cerevisiae]]'' movement of plant genes to fungi 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 airtight.
 
==History of discovery of biological importance of horizontal gene transfer==
 
*The seemingly radical concept of '''horizontal gene transfer''' has a long and interesting pedigree starting in 1946, when Lederberg and Tatum discover genetic conjugation in ''Escherichia coli'' K-12 <ref>Lederberg, J. and Tatum, E. L. (1946). Novel genotypes in mixed cultures of biochemical mutants of bacteria. Cold Spring Habor Symposia of Quantitative Biology. 11, p113.</ref>, and this process was later shown to be carried out by the first recognized [[plasmid]], fertility factor F. In 1951, Joshua and Ester Lederberg , together with Zinder and Lively report the first evidence of bacterial genetic recombination in ''Salmonella'' that was later shown to be caused by bacteriophage mediated [[transduction]] of bacterial chromosome fragments, which is the term used for horizontal movement of genes carried in bacterial viruses. Joshua Lederberg's discovery of conjugation was famously desribed by Salvador Luria (1947) as " to be among the most fundamental advances in the whole history of bacteriological science", giving great prominence to studies of horizontal gene transfer during the 1950s, 60s and 70s <ref>Hayes, W. (1970) The Genetics of Bacteria and their Viruses.2nd Edition, Blackwell.</ref>. Transduction is currently recognized as a major route for horizontal gene movement in bacteria, and plasmid mediated [[bacterial conjugation]] is now known to be promiscuous process that enables DNA to transfer across taxonomic species, genera, phyla and domains.


===Plasmids, episomes, mobile DNA in microorganisms===
===Animals===
* The existence of several genetic structures that can insert within bacterial chomosomes, based on observation of the bacteriophage lambda and fertility factor in 1958 F lead F. Jacob and E. L. Wollman <ref>Jacob, F. and Wollman, E. L. (1958) Les episomes, elements genetiques ajoutes. C. R. Acad, Sci. Paris, 247, p154. </ref> to coin the term '''episome''' for DNA elements that have alternate modes of existence within the cell, either in the chromosome, or as autonomously resplicating stuctures. Subsequent study of these phenomenon revealed numerous occurences of mobile DNA in a wide range of organisms <ref> Berg, D. E. and Howe, M. M. (Eds.)(1989). Mobile DNA. American Society for Microbiology. Washington, D.C.</ref>(such as the presence of '''insertion sequence (IS) "jumping genes"''' that allow F plamid insertion in the chromosome) and widespread horizontal gene transfer involving by bacteriophage, plasmids and mobile DNA in general.
[[Junk DNA]] is the most obvious general evidence of HGT in eukaryotes. Junk DNA is the name given to the seemingly non-functional repetitive DNA sequences that are a major portion of the genomes of many plants and animals. This DNA usually includes multiple copies of various '[[Jumping genes]]' which can proliferate within a genome after they have been transferred from another species. Examples in the human of such mobile elements are 'Hsmar1' and 'Hsmar2' which are related to the widely studied 'mariner' transposon. Close relatives of mariner mobile DNA have been discovered in organisms as diverse as mites, flatworms, hydras, insects, nematodes, mammals and humans.<ref>Robertson HM ''et al.'' (1996) Reconstruction of the ancient 'mariners' of humans. Nat Genet 12:360-361  PMID 8630486</ref> [[Retroviruses]] and [[retrotransposon]]s are other examples of mobile horizontally transferred DNA found in animals.


* Tomoichiro Akiba and Kunitaro Ochia discover '''mobile antibiotic resistance genes''' in bacteria <ref> Ochia, K. Yamanaka, T. Kimura, K. and Sawada, O. (1959). Inheritance of drug resistance (and its transfer) between ''Shigella'' strains and between ''Shigella'' and ''E. coli'' strains. Nihon Iji Shimpo 1861: p34 (In Japanese)</ref>, and the horizontal transfer is later shown to mediated by [[plasmids]] that inject DNA promiscuously into other cells <ref> S. Falcow (1975)Infectious Multiple Drug Resistance. Pion Press, London.</ref>.
The adzuki bean beetle ''Callosobruchus chinensis'' is infected with several strains of bacterial ''Wolbachia'' [[endosymbiont]]s.  A genome fragment of one of these endosymbionts has been found transferred to the X chromosome of the host insect.<ref>Kondo N ''et al.'' (2002)Genome fragment of Wolbachia endosymbiont transferred to X chromosome of host insect.Proc Natl Acad Sci USA  [http://www.pnas.org/cgi/content/full/99/22/14280 99:14280-5] PMID 12386340 (Open access)</ref>


* James Shapiro discovers that spontaneously occuring insertions of large inserts of extra DNA can causes mutationss in the galactose genes of the bacterium ''Escherichia coli'' <ref> Shapiro, J. (1969) Mutations caused by the insertion of genetic material into the galactose operon of ''Escherichia coli''. J. Molec. Biol. 40, p93-109.</ref>. This discovery ultimately led to the discovery of '''mobile inserton sequences (IS)'''.
==History of discovery of HGT==
:: ''See main article [[Horizontal gene transfer (History)]]''
:*''Bacterial genetics starts in 1946''
:: ''see main article [[Horizontal gene transfer in prokaryotes]]
:*''First glimpses of horizontal transfer of traits in plant evolution''
:: '' see also main article [[Barbara McClintock]]
:*''Discovery of mobile genes in flies, and'' ''mariner''
:*''HGT and genetic engineering''


===Horizontal transfer of traits in plant evolution===
==Decoding the tree of life from genomes scrambled by HGT==
* The earliest glimpses that eukaryotic genomes were indeed dynamic structures was obtained by [[Barbara McClintock]] in the 1940s at Cold Spring Harbor Laboratories, New York <ref>. McClintock, B. (1956). Controlling elements in maize. Cold Spring Habor Symposium on Quantitative Biology, 21, p197.</ref>. Her work led to recognition of transposons and other mobile DNAs in plants, which besides being able to move between different locations within a genome, also move between different species. By 1963 the parallels between McClintock's discoveries in maize and genetic instability in bacteria were clearly recognized <ref> Dawson, M. H. and Smith-Keary, P. F. (1963). Episomic control of mutation in ''Salmonella typhimurium''. Heredity, 18, p1.</ref>. By 2003 it was shown that there is '''widespread horizontal transfer of mitochondrial genes among  flowering plants.''' <ref>Bergthorsson U, Adams KL, Thomason B, Palmer JD.(2003) Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature. 2003 Jul 10;424(6945):197-201.</ref> 
: ''For more information, see Citizendium's article on [[Prokaryote phylogeny and evolution]]''


* '''Horizontal gene transfer''' is suggested as an explanation<ref> Went, F. W. (1971). Parallel evolution. Taxon 20: p197-226.</ref> for the fact that similar traits are often shared by unrelated flowering plants, particularly by those sharing the same ecosystems, and for shared traits carried by plants and endophytic fungi that grow on their surfaces. More generally, '''Horizontal gene transfer''' is now widely accepted as '''significant contributer to natural evolution''' in many species<ref>Margaret G. Kidwell (1983)  Evolution of Hybrid Dysgenesis Determinants in ''Drosophila melanogaster''  PNAS  80: 1655-1659.</ref>.
Because each organism carries a record of its ancestry in its DNA, methods for rapid gene isolation and analysis of DNA encoded sequences - which can extract the information from this ancestral archive - have been important for answering questions about evolution, and they have enabled rapid expansion of the field of biological [[systematics]] known as [[Molecular phylogeny|phylogenetic inference]]. Comparison of related ([[homologous]]) gene sequences from different organisms has made it possible to reconstruct the history of many evolutionary lineages.<ref>Steenkamp ET ''et al.'' (2006) The protistan origins of animals and fungi. Mol Biol Evol [http://mbe.oxfordjournals.org/cgi/content/full/23/1/93 23:93-106]  PMID 16151185 (Open access)</ref>
Many issues about evolution have been clarifed by comparing homologous genes from different species, genera, families, and phyla. Unfortunately, HGT complicates the picture, because HGT 'scrambles' the evidence needed to deduce the branching patterns of evolutionary trees. One area of current research in phylogenetic inference, and arguably one of the most challenging problems in evolutionary theory, is the early stages in the [http://tolweb.org/Life_on_Earth/1 evolution of life]. This quandary about the origins of different cell types provides a good illustration of the complications introduced by HGT into the reconstruction of evolutionary history.  


===Discovery of mobile genes in eukaryotes, including mariners===
The main early branches of the tree of life have been intensively studied by [[Microorganism|microbiologists]] because the first organisms were microrganisms. A gene very often used for constructing phylogenetic relationships in microorganisms is the small ribosomal subunit ribosomal RNA (SSU rRNA) gene, as its sequences tend to be conserved among members with close phylogenetic distances, yet it is variable enough that differences can be measured.<ref>Woese C ''et al.'' (1990) Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA [http://www.pnas.org/cgi/reprint/87/12/4576 87:4576-9]  PMID 2112744 (Open access)
*Woese C, Fox G (1977). Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci USA [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=270744 74:5088-90] PMID 270744</ref> The use of SSU rRNA to measure evolutionary "distances" was pioneered by [[Carl Woese]] when formulating the first modern 'tree of life', and his results led him to propose the [[Archaea]] (single celled organisms superficially similar to bacteria) as a third domain (sub-kingdom) of life.


* In February of 1970 wild male fruit-flies from Harbingen, Texas, were discovered to have a second  X sex chromosome (dubbed the MR chromosome) that was inherited in an unusual way, and it also was noticed that this MR chromosome participated on genetic recombination, which does not normally occur in male fruit-flies<ref>Yuichiro Hiraizumi (1971). Spontaneous Recombination in ''Drosophila melanogaster'' Males. Proc. Natl. Acad. Sci. USA 68,268-270.</ref>.( In the fruit fly, (''Drosophila melanogaster'') sex is determined in a similar way to humans as far as the chromosomal make-up is concerned. Males are usually XY - Heterogametic and females homogametic XX.)
[[Image:Tree_phylogeny_3_domain.gif|thumb|300px|left|A three domain representation of the [[phylogenetic tree|tree]] of life based on SSU rRNA sequences, showing the separation of Bacteria, Archaea, and Eukaryote domains. See [[Microorganisms]] article for further explanation]]
Microbiologists introduced the term ''domain'' for the three main early branches of the tree of life, where ''domain'' is  a [[phylogenetic]] term very similar in meaning to biological kingdom. These represent the three main lineages in evolution of early cellular life, and are currently represented by the ''Bacteria'', the ''Archaea'' and ''Eukarya (eukaryote)'' domains. Eukaryotes are all organisms with a well defined nucleus, and this domain comprises protists, fungi, and all organisms in the animal and plant kingdoms, including humans. As seen in the figure (left), studies of SSU rRNA genes (and some other genes) might suggest that ''Archaea'' and ''Eukarya'' have a ''sister'' relationship in evolution, and it has often been assumed that eukaryotes evolved from archaeal cells. However, the fact that genes can move between distant branches of the tree of life even at low probabilities poses problems for scientists trying to reconstruct evolution from studying genes and gene sequences in different organisms due to the scrambling effect of HGT. The challenges are most awkward for the ambitious reconstruction of the earliest branches of the tree of life - because over a long enough time and with large numbers of organisms, many HGT events are certain to have occurred even though each particular transfer event has a low probability.


* '''Mobile DNA in flies'''. This discovery of strange genetics in Drosophila immediately generated interest among geneticists, and during the 1970s, this and similar genetic instabilities of the fruit-fly were intensively investigated. By 1977 is was possible for M. Green to point out that the MR chromosome contained mobile genes (P-elements) that were similar to well characterised mobile DNA of bacteria (for instance [[Insertion sequences]] (IS) and mutator [[bacteriophage Mu]]). Mobile DNA from the MR chromosome had the to move to new chromosomal locations and promote chromosomal aberrations analogous to bacterial mobile DNA.<ref>Green, M. M.  (1977) Genetic Instability in ''Drosophila melanogaster'': De novo Induction of Putative Insertion Mutations.Proc. Nati. Acad. Sci. USA 74, 3490-3493.</ref>
Thus recent discoveries of 'rampant' HGT in microorganisms, and the detection of horizontal movement of genes for SSU rRNA have forced biologists to question the accuracy of at least the early branches in the tree of life, and even to question the validity of trees as useful models of microbial evolution.<ref>Simonson AB ''et al.'' (2005) Decoding the genomic tree of life. Proc Natl Acad Sci USA[http://www.pnas.org/cgi/content/full/102/suppl_1/6608 102 Suppl 1:6608-13] PMID 15851667 (Open access)
*Yap WH ''et al.'' (1999) Distinct types of rRNA operons exist in the genome of the actinomycete ''Thermomonspora chromogena'' and evidence for horizontal gene transfer of an entire rRNA operon. J Bacteriol [http://jb.asm.org/cgi/content/full/181/17/5201?view=long&pmid=10464188 181:5201-9]  PMID 10464188 (Open access)
* Gogarten JP Townsend JP (2005) Horizontal gene transfer, genome innovation and evolution. Nat Rev Microbiol 9:679-87  PMID 16138096</ref>  


* By the early 1980s, Margaret Kidwell and others had already  well documented  the horizontal movement of mobile P genes in fruit fly populations <ref>Margaret G. Kidwell (1983)  Evolution of Hybrid Dysgenesis Determinants in ''Drosophila melanogaster''  PNAS  80: 1655-1659.</ref>,  and the existance of '''horizontal gene transfer in insects''', and the similarity of insect P mobile genes to bacterial mobile genes such as IS that have major natural roles in horizontal gene transfer in bacteria, was firmly established and widely known among professional geneticist.
===Recent efforts to infer evolutionary trees while recognizing HGT===
: ''For more information, see Citizendium's article on [[Evolution of cells]]''


* In 1993 Hugh Robertson reported the widespread but patchy distribution of ''mariner'' mobile DNA in insects, and by 1999 Robertson and others had reported close relatives of this '''mobile DNA in mites, flatworms, hydras, insects, nematodes, mammals and humans.'''
The challenges of ascertaining an accurate branching structure for evolutionary trees of microbes, especially the earliest branches in the tree of life, have been a great spur for current biological research. Clear answers to important questions about these trees are not yet available, but many interesting discoveries and ideas are emerging.


* Subsequent to these discoveries horizontal gene movement has interested a wider audience. Horizontal gene transfer is called by some (Gogarten, 2000)  "A New Paradigm for Biology "  <ref>[http://www.esalenctr.org/display/confpage.cfm?confid=10&pageid=105&pgtype=1]</ref> and emphasised by others as an important factor in "The Hidden Hazards of Genetic Engineering". "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)." <ref>[http://online.sfsu.edu/~rone/GEessays/horizgenetransfer.html]</ref>.
Instead of relying primarily on a single gene such as the SSU rRNA gene to reconstruct evolution, scientific effort has now shifted to exploiting the comprehensive information from the many complete genome sequences of organisms that are now available.<ref>Eisen JA, Fraser CM (2003) Viewpoint phylogenomics: intersection of evolution and genomics. Science 300:1706-7 PMID 12805538
* Fitzpatrick DA ''et al.'' (2006) A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis. BMC Evol Biol[http://www.biomedcentral.com/1471-2148/6/99 6:99]  PMID 17121679 (Open access)
* Ge F ''et al.'' (2005) The Cobweb of Life revealed by genome-scale estimates of horizontal gene transfer. PLoS Biol[http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0030316 3:e316]  PMID 16122348 (Open access)
* Henz SR ''et al.'' (2005) Whole-genome prokaryotic phylogeny.Bioinformatics [http://bioinformatics.oxfordjournals.org/cgi/content/full/21/10/2329 21:2329-35] PMID 15166018 (Open access)
* Urwin R, Maiden MC (2003) Multi-locus sequence typing: a tool for global epidemiology. Trends Microbiol 11:479-87  PMID 14557031</ref> So far, this comparative [[genomics]] approach, made possible by specially developed computer programs and mathematical algorithms, suggests that most of the core genes of bacteria that are useful for deducing evolutionary histories are unaffected by HGT. This confirms the practical experience of microbiologists that consistent and reliable trees can still be deduced for the more recent stages in microbial evolution, such as evolutionary relationships within particular bacterial phyla. This does require, however, using multiple, well chosen genes to investigate how lineages are related to one another. Thus the 'tree' is still a valid metaphor for microbial evolution - but a tree adorned with 'cobwebs' of horizontally transferred genes.  


=== HGT and genetic engineering===
But it is also clear that trees based only on SSU rRNA alone do not capture the events of early eukaryote evolution accurately, and the origins of the first nucleated cells are still uncertain. For instance, careful analysis of the complete genome of the eukaryote yeast shows that many of its genes are more closely related to bacterial genes than they are to archaea, and it is now clear that archaea were not the simple progenitors of the eukaryotes. This discovery is a stark contradiction to earlier findings based on SSU rRNA and limited samples of other genes.<ref>Esser C ''et al.'' (2004) A genome phylogeny for mitochondria among alpha-proteobacteria and a predominantly eubacterial ancestry of yeast nuclear genes. Mol Biol Evol [http://mbe.oxfordjournals.org/cgi/content/full/21/9/1643 21:1643-50] PMID 15155797 (Open access)</ref> (See [[Evolution of cells]] for further discussion.)
* [[Genetic engineering]] itself involves frequent use of '''artificial horizontal gene transfer'''. Molecular cloning technologies ([[genetic engineering]]) were developed in the 1970s using [[plasmids]], the entities involved in much '''natural horizontal gene transfer''' from microorganisms,  as tools to carry foreign DNA inserts in bacteria, and through use of plasmids as genetic engineering [[vectors]] biologists became aquainted with the concept that mammalian genes could function in bacteria, and that bacterial proteins could function in eukaryotes. Mobile DNA such as transposons is now widely used in ''in vivo'' genetic engineering in both bacteria and multicellular organs, but was pioneered by John Beckwith, David Botstein, Nancy Kleckner and John Roth in the 1960s-70s with bacteria.


==Evolutionary theory==
On the other hand, the concept that rampant HGT took place in 'gene-swapping collectives' involved in metabolism and replication at the [[Origin of life|earliest stages of life's origins]], before a postulated transition to Darwinian evolution of the cellular lineages known today, has been used by Carl Woese and colleagues to develop fresh insight into the origins of the universal [[genetic code]].<ref>Goldenfeld N, Woese C (2007) Essays: Connections. Biology's next revolution The emerging picture of microbes as gene–swapping collectives demands a revision of such concepts as organism, species and evolution itself. Nature 445:369 [http://nature.com/nature/focus/arts/connections/index.html doi:10.1038/445369a]  
Horizontal gene transfer is a potential [[Lurking variable|confounding factor]] in inferring [[phylogenetic tree]]s 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.
* Vetsigian K ''et al.'' (2006) Collective evolution and the genetic code. Proc Natl Acad Sci USA [http://www.pnas.org/cgi/content/full/103/28/10696 103:10696–700] PMID 1681888</ref>
 
For example, the most common gene to be used for constructing phylogenetic relationships in [[prokaryote]]s 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.
 
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."  <ref>[http://www.esalenctr.org/display/confpage.cfm?confid=10&pageid=105&pgtype=1]</ref>
 
"Using single [[gene]]s as [[phylogenetic marker]]s, 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." <ref>[http://web.uconn.edu/gogarten/articles/TIG2004_cladogenesis_paper.pdf]</ref>
 
''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 [[eukaryote]]s, 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.
 
Again on p.76, the article continues with:
 
: "The weight of evidence still supports the likelihood that [[mitochondria]] in [[eukaryote]]s derived from alpha-proteobacterial cells and that [[chloroplast]]s 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 cell]]s."
 
The article continues with:
 
:"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.
 
:"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 [[eukaryote]]s)' In other words, early cells, each having relatively few genes, differed in many ways. By swapping [[gene]]s 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."


==See also==
==See also==
*[[Endogenous retrovirus]]
*[[Gene flow]]
*[[Species]]
*[[Phylogenetic tree]]
*[[Evolution of cells]]
*[[Germline]]
*[[Germline]]
*[[Systems biology]]
*[[Origin of life]]
*[[Mitochondrion]]
*[[Mitochondrion]]
*[[HeLa]]
*[[Endosymbiont]]
*[[Endosymbiotic theory]]
*[[Integron]]
*[[Integron]]
*[[Virus]]
*[[Provirus]]
*[[Provirus]]
*[[Retrotransposon]]
*[[Retrotransposon]]
*[[Rhizome (philosophy)]]
*[[Endogenous retrovirus]]
*[[Plasmid]]
*[[Mobile DNA]]
*[[Pilus]]
*[[Transgenic plant]]


==References==
==References==
<references/>
====Citations====
 
<div class="references-small" style="-moz-column-count:2; column-count:2;">
 
<references />
==Further Reading==
</div>
* 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. 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. [http://www.cbcb.umd.edu/~salzberg/docs/ScienceLateralTransfer.pdf] (Free full article)
* This article seeks to shift the emphasis in early [[Phylogenetics|phylogenic adaptation]] from vertical to horizontal gene transfer. Woese, Carl (2002) "On the evolution of cells", PNAS, 99(13) 8742-8747. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=12077305] (Free full article)
* This article gives convincing evidence of horizontal transfer of bacterial DNA to ''Saccharomyces cerevisiae'' "Contribution of Horizontal Gene Transfer to the Evolution of Saccharomyces cerevisiae." Hall C, Brachat S, Dietrich FS. Eukaryot Cell 2005 Jun 4(6):1102-15. [http://ec.asm.org/cgi/content/full/4/6/1102]
* This book provides a comprehensive discussion of mobile DNA, jumping genes, transposons and the like in many organisms, not only bacteria. Berg, Douglas E. and Howe, Martha M. (Eds.)(1989). "Mobile DNA". American Society for Microbiology. Washington, D.C.
* This article gives evidence, but does not conclusively prove, that ''[[Wolbachia]]'' DNA is in the [[Callosobruchus chinensis|azuki bean beetle]] genome (a species of [[bean weevil]]). 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". [http://www.pubmedcentral.gov/articlerender.fcgi?tool=pubmed&pubmedid=12386340] (Free full article)
* 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. Snel B, Bork P, Huynen MA (1999) "Genome phylogeny based on gene content", Nature Genetics, 21(1) 66-67. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=9916801&dopt=Abstract]
* Webfocus in Nature with free review articles [http://www.nature.com/nrmicro/focus/genetransfer/index.html]
* Uprooting the Tree of Life by W. Ford Doolitte (Scientific American, February 2000, pp 72-77)
 
==External links==
*[http://www.esalenctr.org/display/confpage.cfm?confid=10&pageid=105&pgtype=1  Horizontal Gene Transfer - A New Paradigm for Biology]
*[http://opbs.okstate.edu/~melcher/MG/MGW3/MG334.html Horizontal Gene Transfer (page 334 of Molecular Genetics by Ulrich Melcher)]
*[http://www.i-sis.org.uk/ireaff99.php Report on horizontal gene transfer by Mae-Wan Ho, March 22, 1999]
*[http://www.i-sis.org.uk/FSAopenmeeting.php Recent Evidence Confirms Risks of Horizontal Gene Transfer]
*[http://www.sci.sdsu.edu/~smaloy/MicrobialGenetics/topics/genetic-exchange/exchange/exchange.html  Horizontal Gene Transfer at sciences.sdsu.edu]
*[http://www.pnas.org/cgi/content/abstract/96/7/3801 Horizontal gene transfer among genomes: The complexity hypothesis Vol. 96, Issue 7, 3801-3806, March 30, 1999 of The National Academy of Sciences]
*[http://www.stat.rice.edu/~mathbio/Ochman2000.pdf PDF article on Horizontal Gene Transfer]
*[http://cryptome.org/smallpox-wmd.htm 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.'"
*[http://mic.sgmjournals.org/cgi/content/full/145/12/3321 Retrotransfer or gene capture: a feature of conjugative plasmids, with ecological and evolutionary significance]


[[Category:Genetics]]
====Further reading====
[[Category:CZ Live]]
*[http://www.nature.com/nrmicro/focus/genetransfer/index.html Focus on horizontal gene transfer] Webfocus in ''Nature'' with free access review articles.
*[http://cryptome.org/smallpox-wmd.htm Smallpox knows how to make a mouse protein. How did smallpox learn that?] ''The New Yorker'' July 12, 1999, p44-61. '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'. (Open access)
* ''[http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0030169  Where Do All Those Genes Come From?]'' This study resolves a long-standing paradox: how is it possible to deduce reliable evolutionary histories from gene sequences in bacteria despite extensive HGT? (Open access)
* Woese C (2002) [http://www.pnas.org/cgi/content/full/99/13/8742 On the evolution of cells.]Proc Natl Acad Sci USA 99:8742-7  PMID 12077305. This article shifts the emphasis in early phylogenic adaptation from vertical to horizontal gene transfer. (Open access)
* Salzberg SL ''et al.'' (2001) [http://www.cbcb.umd.edu/~salzberg/docs/ScienceLateralTransfer.pdf Microbial genes in the human genome: lateral transfer or gene loss?] Science 292:1903-6 PMID 11358996. This reports that one dramatic claim of HGT - in which a distinguished group of scientists claimed that bacteria transferred their DNA directly into the human lineage - was simply wrong. (Open access)
* Jain R ''et al.'' Horizontal gene transfer among genomes: the complexity hypothesis. Proc Natl Acad Sci USA [http://www.pnas.org/cgi/content/abstract/96/7/3801 96:3801-6]  PMID 10097118 (Open access)
* Hall C ''et al.'' (2005) Contribution of horizontal gene transfer to the evolution of ''Saccharomyces cerevisiae''. Eukaryot Cell [http://ec.asm.org/cgi/content/full/4/6/1102 4:1102-15] PMID 15947202 Convincing evidence of horizontal transfer of bacterial DNA into yeast. (Open access.)
* Zhu J ''et al.'' (2000) The bases of crown gall tumorigenesis.J Bacteriol [http://jb.asm.org/cgi/content/full/182/14/3885?view=long&pmid=10869063  182:3885-95] PMID 10869063  This article describes the biology of crown-gall bacterium, and the mechanism of DNA injection by this bacterium, and explains how genes can move between bacterial species and from bacteria to eukaryotic organisms, and illustrates the extent to which different species can co-evolve. (Open access)
* ''Horizontal Gene Transfer'' Syvanen M, Kado CI (2002) 2nd edition, Academic Press ISBN 0-12-680126-6  A comprehensive treatise. [http://www.nature.com/hdy/journal/v90/n1/full/6800196a.html Reviewed here by M-W Ho]
* ''Acquiring genomes: a theory of the origin of species.'' Margulis L and Sagan D (2002) Basic Books ISBN 0-465-04392-5. A book that looks at gene transfer from a different perspective to many conventional interpretations, but with an emphasis on microbial diversity. [http://home.planet.nl/~gkorthof/korthof72.htm Reviewed here.]
* Richardson AO, Palmer, JD (2007) Horizontal gene transfer in plants. J Exp Bot 58:1–9 doi:10.1093/jxb/erl148  PMID 17030541
* Gogarten JP Townsend JP (2005) Horizontal gene transfer, genome innovation and evolution. Nat Rev Microbiol 9:679-87 PMID 16138096. One article in a whole issue of the journal ''Nature Reviews Microbiology'' largely devoted to HGT.
* Weinbauer MG, Rassoulzadegan F (2004) Are viruses driving microbial diversification and diversity? Envir Microbiol [http://www.blackwell-synergy.com/links/doi/10.1046/j.1462-2920.2003.00539.x/full/ 6:1-11 ] PMID 14686936 Discussion of both the evolutionary and ecological activities of viruses in the ocean, a major source of HGT in nature.


[[de:Horizontaler Gentransfer]]
====External links====
[[nl:Genetische uitwisseling]]
* [http://opbs.okstate.edu/~melcher/MG/MGW3/MG334.html Horizontal gene transfer] (p334 of Molecular Genetics by Ulrich Melcher).
[[ja:遺伝子の水平伝播]]
*[http://www.sci.sdsu.edu/~smaloy/MicrobialGenetics/topics/genetic-exchange/exchange/exchange.html  Horizontal gene transfer at sciences.sdsu.edu]
[[ru:Конъюгация]]
*[http://www.stat.rice.edu/~mathbio/Ochman2000.pdf Lateral gene transfer and the nature of bacterial innovation (pdf), Ochman ''et al.'' (2000)]
* [http://gogarten.uconn.edu/ Gogarten Laboratory Webpages.]
*[http://www.esalenctr.org/display/confpage.cfm?confid=10&pageid=105&pgtype=1  Horizontal gene transfer - A new paradigm for biology]
*[http://www.i-sis.org.uk/ireaff99.php Report on horizontal gene transfer] by Mae-Wan Ho, 1999
*[http://www.i-sis.org.uk/FSAopenmeeting.php Recent evidence confirms risks of horizontal gene transfer]
<br/>

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Legionella pneumophila are prokaryotic bacteria that can survive and reproduce inside phagocytic cells such as protists that have eaten them. They are competent in DNA transformation and occasionally capture genes from their eukaryotic host cells.

Horizontal gene transfer occurs when an organism transfers its genetic material to a being other than one of its own offspring. The actual process of this transfer can be by any mechanism, but because genes are not passing by descent, horizontal gene transfer (abbreviated as HGT) is always very different from vertical gene transfer. In vertical descent, parental traits are inherited by progeny by one of two general methods: either (1) sexual reproduction in which gametes form zygotes, a common method in higher animals and plants, or (2) by asexual reproduction, where splitting of cells or an entire organism grows from a fragment, as is usual in bacteria and fungi, but which also happens in some animals and plants. HGT is a much more recently discovered route of passage for genetic material; it is relatively common in microorganisms, and to a lesser extent in plants. By HGT, genetic material can be shared between organisms without the immediate relatedness of mother cell to daughter cells, or parent organisms to offspring; indeed, by HGT material can pass between organismsthat are not even be of the same species, genus, sub-kingdom or kingdom of life form. HGT (sometimes called lateral gene transfer) is very much less common than vertical gene transfer, so its detection requires special techniques.

Introduction

Evidence from genome science and bioinformatics shows that HGT has occurred between diverse biological taxa that are widely separated in the phylogenetic tree of life. Known HGTs include movement of genetic material between different species of microbes and other microbial taxa such as protists, gene movement between different plant families, between different animals, and between bacteria and plants.

HGT — gene exchange between non-related organisms —appears commonplace among bacteria, but contributes just small fragments of genetic information, leaving the traditional tree of life intact. From: Comparing Gene Trees and Genome Trees: A Cobweb of Life? PLoS Biol 3:e347

Microorganisms appear to be most affected by HGT, but even in microbes only about 2% of core genes are transferred laterally. Because this percentage is so low, the main lineages of microbial evolution can still be treated as 'trees' branched by vertical descent, with HGT included in the scheme only as 'cobwebs' (see figure at right).

Gene transfers between different biological sub-kingdoms (domains), such as between eukaryotic protists and bacteria, or between bacteria and insects are the most phylogenetically extreme cases of HGT. An example is bacterial 'rol' genes from Agrobacterium species which have been found in tobacco plants (Nicotiniana).[1]

HGT is just one of several processes that can cause rearrangement of genomes during evolution. The possibility of intracellular movement of genes between different parts of an organism's genome (that is, between the chromosomes of the nucleus, the circular mitochondrion chromosome, or the circular plastid (chloroplast) chromosome) needs to be considered when evaluating HGT between different species.[2]

Main features of HGT in nature

  • A hallmark of HGT is the presence of the same gene in organisms that are only very distantly related to each other. The frequent discovery of shared DNA sequences such as the mariner class of transposons, insertion sequence DNA, retrovirus genes in diverse species and shared mitochondrial genes in diverse flowering plants indicate that mobile DNA has natural pathways for movement between species. (The name mariner for a class of related transposons is an allusion to The Rime of the Ancient Mariner, meaning a traveller to distant lands.) Close relatives of mariner mobile DNA have been identified in organisms as diverse as mites, flatworms, hydras, insects, nematodes, mammals and humans.[3]
Millet. From: Jumping Genes Cross Plant Species Boundaries.Analysis of the genomes of millet and rice revealed evidence for HGT between chromosomes in the nucleus of one plant to chromosomes in the nucleus of a reproductively isolated species
  • Horizontal movement of genes is common among bacteria, and is a major factor in accelerating the rate of their evolution. HGT is involved in multiple-antibiotic resistance in pathogenic bacteria, and this is a major factor that is limiting the effectiveness of antibiotics. Inter-domain (sub-kingdom) transfer of several genes from eukaryotes to bacteria for instance, has occurred in the 'accidentally pathogenic' bacterium (Legionella pneumophila, see illustration) that lives within vacuoles of protist and mammalian macrophage cells.[4]
  • HGT is documented in diverse unicellular protists, which can contain several genes transferred from both prokaryotes and other protists.[5]
  • HGT occurs globally on a massive scale among marine microorganisms. Viruses, which, at total numbers near 1029 are the most common biological entities in the sea, are a major pathway for gene movement between different species. It has been estimated that, on average, 1013 virus-mediated gene transfer events occur in the Mediterranean sea each year. Endosymbiosis with an alga is identified as a route for HGT in marine dinoflagellates, the organisms that cause 'red tides'.[6]
  • Interspecies gene movement by cross-hybridization is common in flowering plants. Mechanisms for HGT in flowering plants between more distant taxa involving parasitic plants such as dodder and endophytes (such as mosses, which are in intimate cell-to-cell contact with their host plants) are also well established (see Horizontal gene transfer in plants). Plant mitochondria can be unusually active in HGT.
  • Not all of the ways in which HGT occurs are fully characterized, but some have been identified. HGT is hard to detect directly, as it is relatively rare within a species, but can be detected by modern DNA analysis which can enable detailed comparison of genomes. In insects, mites and viruses are probably vectors for HGT. In certain bacteria, surface appendages called pili have various roles in DNA uptake, DNA secretion and DNA transfer which have been extensively analyzed; HGT in bacteria includes plasmid-mediated promiscuous mating by bacteria (for instance by the crown-gall bacterium Agrobacterium tumefaciens) and carriage of genes between species by viruses. Direct DNA uptake is another transfer mechanism, as illustrated by Legionella bacteria, which are naturally competent for DNA uptake.

Prokaryotes

See main article HGT in prokaryotes
The three main mechanisms of HGT in bacteria and archaea discussed here are:

Eukaryotes

See also Endosymbiotic theory

Protists

Analysis of the complete genome sequence of the protist Entamoeba histolytica indicates 96 cases of relatively recent HGT from prokaryotes. There is also convincing evidence that a bacterial gene for a biosynthetic enzyme has been recruited by the protist Trichomonas vaginalis from bacteria related to the ancestors of Pasteurella bacteria. Similar analysis of the protist Cryptosporidium parvum reveals 24 candidates of HGT from bacteria. These results fit the idea that 'you are what you eat'. That is, in unicellular grazing organisms, foreign genetic material is constantly entering the cell from food organisms, and occasionally some of this material enters the genome.[7]

Fungi

Comparison of the genome sequences of two fungi, baker's yeast (Saccharomyces cerevisiae) and Ashbya gossypii, has shown that Saccharomyces has received two genes from bacteria by HGT. One of these genes codes for an enzyme that allows baker's yeast to make pyrimidine nucleotide bases anaerobically, and the other allows usage of sulfur from several organic sulfur sources. Other work with yeasts suggests that eight genes from Yarrowia lipolytica, five from Kluyveromyces lactis, and one from Debaryomyces hansenii are horizontally transferred.[8]

Other eukaryotes

Analysis of DNA sequences suggests that HGT has also occurred within multicellular eukaryotes, by a route that involves transfer of genes from chloroplast and mitochondrial genomes to the nuclear genomes.[9] According to the endosymbiotic theory, chloroplasts and mitochondria originated as the bacterial endosymbionts of a progenitor to the eukaryotic cell, and endosymbiosis can be considered to be a special case of HGT.

Plants

See Horizontal gene transfer in plants for
  • Natural gene transfer between plants that do not cross-pollinate
  • Jumping genes cross naturally between rice and millet
  • Epiphytes and parasites as a bridge for gene flow between diverse plant species
See Transgenic plant for hybridization by cross-pollination and artificial horizontal gene transfer in biotechnology.

It has also been discovered that plant genes can move to endophyte fungi that grow on them. Several plant endophyte fungi that grow on taxol-producing yew trees have gained the ability to make taxol themselves.[10] (Taxol, also called paclitaxel, is an anti-cancer drug found in yew trees.)

Animals

Junk DNA is the most obvious general evidence of HGT in eukaryotes. Junk DNA is the name given to the seemingly non-functional repetitive DNA sequences that are a major portion of the genomes of many plants and animals. This DNA usually includes multiple copies of various 'Jumping genes' which can proliferate within a genome after they have been transferred from another species. Examples in the human of such mobile elements are 'Hsmar1' and 'Hsmar2' which are related to the widely studied 'mariner' transposon. Close relatives of mariner mobile DNA have been discovered in organisms as diverse as mites, flatworms, hydras, insects, nematodes, mammals and humans.[11] Retroviruses and retrotransposons are other examples of mobile horizontally transferred DNA found in animals.

The adzuki bean beetle Callosobruchus chinensis is infected with several strains of bacterial Wolbachia endosymbionts. A genome fragment of one of these endosymbionts has been found transferred to the X chromosome of the host insect.[12]

History of discovery of HGT

See main article Horizontal gene transfer (History)
  • Bacterial genetics starts in 1946
see main article Horizontal gene transfer in prokaryotes
  • First glimpses of horizontal transfer of traits in plant evolution
see also main article Barbara McClintock
  • Discovery of mobile genes in flies, and mariner
  • HGT and genetic engineering

Decoding the tree of life from genomes scrambled by HGT

For more information, see Citizendium's article on Prokaryote phylogeny and evolution

Because each organism carries a record of its ancestry in its DNA, methods for rapid gene isolation and analysis of DNA encoded sequences - which can extract the information from this ancestral archive - have been important for answering questions about evolution, and they have enabled rapid expansion of the field of biological systematics known as phylogenetic inference. Comparison of related (homologous) gene sequences from different organisms has made it possible to reconstruct the history of many evolutionary lineages.[13] Many issues about evolution have been clarifed by comparing homologous genes from different species, genera, families, and phyla. Unfortunately, HGT complicates the picture, because HGT 'scrambles' the evidence needed to deduce the branching patterns of evolutionary trees. One area of current research in phylogenetic inference, and arguably one of the most challenging problems in evolutionary theory, is the early stages in the evolution of life. This quandary about the origins of different cell types provides a good illustration of the complications introduced by HGT into the reconstruction of evolutionary history.

The main early branches of the tree of life have been intensively studied by microbiologists because the first organisms were microrganisms. A gene very often used for constructing phylogenetic relationships in microorganisms is the small ribosomal subunit ribosomal RNA (SSU rRNA) gene, as its sequences tend to be conserved among members with close phylogenetic distances, yet it is variable enough that differences can be measured.[14] The use of SSU rRNA to measure evolutionary "distances" was pioneered by Carl Woese when formulating the first modern 'tree of life', and his results led him to propose the Archaea (single celled organisms superficially similar to bacteria) as a third domain (sub-kingdom) of life.

A three domain representation of the tree of life based on SSU rRNA sequences, showing the separation of Bacteria, Archaea, and Eukaryote domains. See Microorganisms article for further explanation

Microbiologists introduced the term domain for the three main early branches of the tree of life, where domain is a phylogenetic term very similar in meaning to biological kingdom. These represent the three main lineages in evolution of early cellular life, and are currently represented by the Bacteria, the Archaea and Eukarya (eukaryote) domains. Eukaryotes are all organisms with a well defined nucleus, and this domain comprises protists, fungi, and all organisms in the animal and plant kingdoms, including humans. As seen in the figure (left), studies of SSU rRNA genes (and some other genes) might suggest that Archaea and Eukarya have a sister relationship in evolution, and it has often been assumed that eukaryotes evolved from archaeal cells. However, the fact that genes can move between distant branches of the tree of life even at low probabilities poses problems for scientists trying to reconstruct evolution from studying genes and gene sequences in different organisms due to the scrambling effect of HGT. The challenges are most awkward for the ambitious reconstruction of the earliest branches of the tree of life - because over a long enough time and with large numbers of organisms, many HGT events are certain to have occurred even though each particular transfer event has a low probability.

Thus recent discoveries of 'rampant' HGT in microorganisms, and the detection of horizontal movement of genes for SSU rRNA have forced biologists to question the accuracy of at least the early branches in the tree of life, and even to question the validity of trees as useful models of microbial evolution.[15]

Recent efforts to infer evolutionary trees while recognizing HGT

For more information, see Citizendium's article on Evolution of cells

The challenges of ascertaining an accurate branching structure for evolutionary trees of microbes, especially the earliest branches in the tree of life, have been a great spur for current biological research. Clear answers to important questions about these trees are not yet available, but many interesting discoveries and ideas are emerging.

Instead of relying primarily on a single gene such as the SSU rRNA gene to reconstruct evolution, scientific effort has now shifted to exploiting the comprehensive information from the many complete genome sequences of organisms that are now available.[16] So far, this comparative genomics approach, made possible by specially developed computer programs and mathematical algorithms, suggests that most of the core genes of bacteria that are useful for deducing evolutionary histories are unaffected by HGT. This confirms the practical experience of microbiologists that consistent and reliable trees can still be deduced for the more recent stages in microbial evolution, such as evolutionary relationships within particular bacterial phyla. This does require, however, using multiple, well chosen genes to investigate how lineages are related to one another. Thus the 'tree' is still a valid metaphor for microbial evolution - but a tree adorned with 'cobwebs' of horizontally transferred genes.

But it is also clear that trees based only on SSU rRNA alone do not capture the events of early eukaryote evolution accurately, and the origins of the first nucleated cells are still uncertain. For instance, careful analysis of the complete genome of the eukaryote yeast shows that many of its genes are more closely related to bacterial genes than they are to archaea, and it is now clear that archaea were not the simple progenitors of the eukaryotes. This discovery is a stark contradiction to earlier findings based on SSU rRNA and limited samples of other genes.[17] (See Evolution of cells for further discussion.)

On the other hand, the concept that rampant HGT took place in 'gene-swapping collectives' involved in metabolism and replication at the earliest stages of life's origins, before a postulated transition to Darwinian evolution of the cellular lineages known today, has been used by Carl Woese and colleagues to develop fresh insight into the origins of the universal genetic code.[18]

See also

References

Citations

  1. ↑ de Felipe K et al. (2005) Evidence for acquisition of Legionella type IV secretion substrates via interdomain horizontal gene transfer. J Bacteriol 187:7716-26 PMID 16267296 (Open access)
    • Kondo N et al. (2002) Genome fragment of Wolbachia endosymbiont transferred to X chromosome of host insect. Proc Natl Acad Sci USA 99:14280-5 PMID 12386340 (Open access)
    • Intrieri MC, Buiatti M (2001) The horizontal transfer of Agrobacterium rhizogenes genes and the evolution of the genus Nicotiana. Mol Phylogen Evol 20:100-10 PMID 11421651
  2. ↑ Timmis JN et al. (2004) Endosymbiotic gene transfer: organelle genomes forge eukaryotic chromosomes. Nat Rev Genet 5:123-35 PMID 14735123
  3. ↑ Robertson HM (1996) Reconstruction of the ancient mariners of humans. Nat Genet 12:360-1 PMID 8630486
  4. ↑ Jain R et al. (2003) Horizontal gene transfer accelerates genome innovation and evolution. Mol Biol Evol 20:1598-602 PMID 12777514 (Open access)
    • de Felipe KS et al. (2005) Evidence for acquisition of Legionella type IV secretion substrates via interdomain horizontal gene transfer. J Bacteriol187:7716-26 PMID 16267296 (Open access)
  5. ↑ Andersson JO et al. (2006) Evolution of four gene families with patchy phylogenetic distributions: influx of genes into protist genomes.BMC Evol Biol PMID 16551352 (Open access)
    • Loftus B et al. (2005) The genome of the protist parasite Entamoeba histolytica. Nature 433:865-8 PMID 15729342
  6. ↑ Fuhrman JA (1999) Marine viruses and their biogeochemical and ecological effects. Nature 399:541–8 PMID 10376593
    • Yoon HS et al. (2005) Tertiary endosymbiosis driven genome evolution in dinoflagellate algae. Mol Biol Evol 22:1299-308 PMID 15746017 (Open access)
  7. ↑ Loftus B et al. (2005) The genome of the protist parasite Entamoeba histolytica. Nature 433:865-8 PMID 15729342
    • Doolittle WF (1998) You are what you eat: a gene transfer ratchet could account for bacterial genes in eukaryotic nuclear genomes. Trends in Genetics 14:307-11 PMID 9724962
  8. ↑ Dujon B et al. {2004) Genome evolution in yeasts. Nature 430:35-44 PMID 15229592
  9. ↑ Adams KL Palmer JD (2003) Evolution of mitochondrial gene content: gene loss and transfer to the nucleus. Mol Phylogenet Evol 29:380–95 PMID 14615181
  10. ↑ Shrestha K et al. (2001) Evidence for paclitaxel from three new endophytic fungi of Himalayan yew of Nepal. Planta Med 67:374-6 PMID 11458463
  11. ↑ Robertson HM et al. (1996) Reconstruction of the ancient 'mariners' of humans. Nat Genet 12:360-361 PMID 8630486
  12. ↑ Kondo N et al. (2002)Genome fragment of Wolbachia endosymbiont transferred to X chromosome of host insect.Proc Natl Acad Sci USA 99:14280-5 PMID 12386340 (Open access)
  13. ↑ Steenkamp ET et al. (2006) The protistan origins of animals and fungi. Mol Biol Evol 23:93-106 PMID 16151185 (Open access)
  14. ↑ Woese C et al. (1990) Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 87:4576-9 PMID 2112744 (Open access)
    • Woese C, Fox G (1977). Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci USA 74:5088-90 PMID 270744
  15. ↑ Simonson AB et al. (2005) Decoding the genomic tree of life. Proc Natl Acad Sci USA102 Suppl 1:6608-13 PMID 15851667 (Open access)
    • Yap WH et al. (1999) Distinct types of rRNA operons exist in the genome of the actinomycete Thermomonspora chromogena and evidence for horizontal gene transfer of an entire rRNA operon. J Bacteriol 181:5201-9 PMID 10464188 (Open access)
    • Gogarten JP Townsend JP (2005) Horizontal gene transfer, genome innovation and evolution. Nat Rev Microbiol 9:679-87 PMID 16138096
  16. ↑ Eisen JA, Fraser CM (2003) Viewpoint phylogenomics: intersection of evolution and genomics. Science 300:1706-7 PMID 12805538
    • Fitzpatrick DA et al. (2006) A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis. BMC Evol Biol6:99 PMID 17121679 (Open access)
    • Ge F et al. (2005) The Cobweb of Life revealed by genome-scale estimates of horizontal gene transfer. PLoS Biol3:e316 PMID 16122348 (Open access)
    • Henz SR et al. (2005) Whole-genome prokaryotic phylogeny.Bioinformatics 21:2329-35 PMID 15166018 (Open access)
    • Urwin R, Maiden MC (2003) Multi-locus sequence typing: a tool for global epidemiology. Trends Microbiol 11:479-87 PMID 14557031
  17. ↑ Esser C et al. (2004) A genome phylogeny for mitochondria among alpha-proteobacteria and a predominantly eubacterial ancestry of yeast nuclear genes. Mol Biol Evol 21:1643-50 PMID 15155797 (Open access)
  18. ↑ Goldenfeld N, Woese C (2007) Essays: Connections. Biology's next revolution The emerging picture of microbes as gene–swapping collectives demands a revision of such concepts as organism, species and evolution itself. Nature 445:369 doi:10.1038/445369a

Further reading

  • Focus on horizontal gene transfer Webfocus in Nature with free access review articles.
  • Smallpox knows how to make a mouse protein. How did smallpox learn that? The New Yorker July 12, 1999, p44-61. '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'. (Open access)
  • Where Do All Those Genes Come From? This study resolves a long-standing paradox: how is it possible to deduce reliable evolutionary histories from gene sequences in bacteria despite extensive HGT? (Open access)
  • Woese C (2002) On the evolution of cells.Proc Natl Acad Sci USA 99:8742-7 PMID 12077305. This article shifts the emphasis in early phylogenic adaptation from vertical to horizontal gene transfer. (Open access)
  • Salzberg SL et al. (2001) Microbial genes in the human genome: lateral transfer or gene loss? Science 292:1903-6 PMID 11358996. This reports that one dramatic claim of HGT - in which a distinguished group of scientists claimed that bacteria transferred their DNA directly into the human lineage - was simply wrong. (Open access)
  • Jain R et al. Horizontal gene transfer among genomes: the complexity hypothesis. Proc Natl Acad Sci USA 96:3801-6 PMID 10097118 (Open access)
  • Hall C et al. (2005) Contribution of horizontal gene transfer to the evolution of Saccharomyces cerevisiae. Eukaryot Cell 4:1102-15 PMID 15947202 Convincing evidence of horizontal transfer of bacterial DNA into yeast. (Open access.)
  • Zhu J et al. (2000) The bases of crown gall tumorigenesis.J Bacteriol 182:3885-95 PMID 10869063 This article describes the biology of crown-gall bacterium, and the mechanism of DNA injection by this bacterium, and explains how genes can move between bacterial species and from bacteria to eukaryotic organisms, and illustrates the extent to which different species can co-evolve. (Open access)
  • Horizontal Gene Transfer Syvanen M, Kado CI (2002) 2nd edition, Academic Press ISBN 0-12-680126-6 A comprehensive treatise. Reviewed here by M-W Ho
  • Acquiring genomes: a theory of the origin of species. Margulis L and Sagan D (2002) Basic Books ISBN 0-465-04392-5. A book that looks at gene transfer from a different perspective to many conventional interpretations, but with an emphasis on microbial diversity. Reviewed here.
  • Richardson AO, Palmer, JD (2007) Horizontal gene transfer in plants. J Exp Bot 58:1–9 doi:10.1093/jxb/erl148 PMID 17030541
  • Gogarten JP Townsend JP (2005) Horizontal gene transfer, genome innovation and evolution. Nat Rev Microbiol 9:679-87 PMID 16138096. One article in a whole issue of the journal Nature Reviews Microbiology largely devoted to HGT.
  • Weinbauer MG, Rassoulzadegan F (2004) Are viruses driving microbial diversification and diversity? Envir Microbiol 6:1-11 PMID 14686936 Discussion of both the evolutionary and ecological activities of viruses in the ocean, a major source of HGT in nature.

External links


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