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Horizontal gene transfer (HGT) or lateral gene transfer (LGT) is the movement of genetic material between
unicellular A unicellular organism, also known as a single-celled organism, is an organism In biology, an organism () is any organic, life, living system that functions as an individual entity. All organisms are composed of cells (cell theory). Or ...
and/or
multicellular organism A multicellular organism is an organism In biology, an organism () is any organic, life, living system that functions as an individual entity. All organisms are composed of cells (cell theory). Organisms are classified by taxonomy (biol ...
s other than by the ("vertical") transmission of
DNA Deoxyribonucleic acid (; DNA) is a molecule File:Pentacene on Ni(111) STM.jpg, A scanning tunneling microscopy image of pentacene molecules, which consist of linear chains of five carbon rings. A molecule is an electrically neutral gro ...

DNA
from parent to offspring (
reproduction Reproduction (or procreation or breeding) is the biological process Biological processes are those processes that are vital for an organism In biology, an organism (from Ancient Greek, Greek: ὀργανισμός, ''organismos'') is ...

reproduction
). HGT is an important factor in the evolution of many organisms. Horizontal gene transfer is the primary mechanism for the spread of
antibiotic resistance Antimicrobial resistance (AMR or AR) occurs when microbe A microorganism, or microbe,, ''mikros'', "small") and ''organism'' from the el, ὀργανισμός, ''organismós'', "organism"). It is usually written as a single word but is some ...

antibiotic resistance
in bacteria, and plays an important role in the evolution of
bacteria Bacteria (; common noun bacteria, singular bacterium) are ubiquitous, mostly free-living organisms often consisting of one Cell (biology), biological cell. They constitute a large domain (biology), domain of prokaryotic microorganisms. Typ ...

bacteria
that can degrade novel compounds such as human-created
pesticides Pesticides are substances that are meant to control pest (organism), pests. The term pesticide includes all of the following: herbicide, insecticides (which may include insect growth regulators, termiticides, etc.) nematicide, molluscicide, pi ...
and in the evolution, maintenance, and transmission of
virulence Virulence is a pathogen's or microorganism's ability to cause damage to a host. In most contexts, especially in animal systems, virulence refers to the degree of damage caused by a microbe to its host (biology), host. The Pathogen#Pathogenicity, ...
. It often involves
temperate In geography Geography (from Greek Greek may refer to: Greece Anything of, from, or related to Greece Greece ( el, Ελλάδα, , ), officially the Hellenic Republic, is a country located in Southeast Europe. Its populati ...
bacteriophage A bacteriophage (), also known informally as a ''phage'' (), is a virus A virus is a that only inside the living of an . Viruses infect all , from animals and plants to s, including and . Since 's 1892 article describing a non-b ...

bacteriophage
s and
plasmids A plasmid is a small, extrachromosomal DNA molecule within a cell that is physically separated from chromosomal DNA and can replicate independently. They are most commonly found as small circular, double-stranded DNA molecules in bacteria; how ...

plasmids
. Genes responsible for antibiotic resistance in one species of bacteria can be transferred to another species of bacteria through various mechanisms of HGT such as
transformation Transformation may refer to: Science and mathematics In biology and medicine * Metamorphosis, the biological process of changing physical form after birth or hatching * Malignant transformation, the process of cells becoming cancerous * Transf ...
, and
conjugation Conjugation or conjugate may refer to: Linguistics * Grammatical conjugation, the modification of a verb from its basic form * Emotive conjugation or Russell's conjugation, the use of loaded language Mathematics * Complex conjugation, the change ...
, subsequently arming the antibiotic resistant genes' recipient against antibiotics. The rapid spread of antibiotic resistance genes in this manner is becoming medically challenging to deal with. Ecological factors may also play a role in the HGT of antibiotic resistant genes. It is also postulated that HGT promotes the maintenance of a universal life biochemistry and, subsequently, the universality of the genetic code. Most thinking in
genetics Genetics is a branch of biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactions, Physiology, ...

genetics
has focused upon vertical transfer, but the importance of horizontal gene transfer among single-cell organisms is beginning to be acknowledged.
Gene delivery Gene delivery is the process of introducing foreign gene delivery, such as DNA or RNA, into host cells. Gene delivery must reach the genome In the fields of molecular biology and genetics Genetics is a branch of biology concerned ...
can be seen as an artificial horizontal gene transfer, and is a form of
genetic engineering Genetic engineering, also called genetic modification or genetic manipulation, is the direct manipulation of an organism's gene In biology, a gene (from ''genos'' "...Wilhelm Johannsen coined the word gene to describe the Mendelian_in ...
.


History

Griffith's experiment Griffith's experiment, reported in 1928 by Frederick Griffith Frederick Griffith (1877–1941) was a British bacteriologist A bacteriologist is a microbiologist or a professional trained in bacteriology, a subdivision of microbiology. The d ...
, reported in 1928 by
Frederick Griffith Frederick Griffith (1877–1941) was a British bacteriologist A bacteriologist is a microbiologist or a professional trained in bacteriology, a subdivision of microbiology. The duties of a bacteriologist include prevention, diagnosis and prog ...
, was the first experiment suggesting that bacteria are capable of transferring genetic information through a process known as
transformation Transformation may refer to: Science and mathematics In biology and medicine * Metamorphosis, the biological process of changing physical form after birth or hatching * Malignant transformation, the process of cells becoming cancerous * Transf ...
. Griffith's findings were followed by research in the late 1930s and early 40s that isolated
DNA Deoxyribonucleic acid (; DNA) is a molecule File:Pentacene on Ni(111) STM.jpg, A scanning tunneling microscopy image of pentacene molecules, which consist of linear chains of five carbon rings. A molecule is an electrically neutral gro ...

DNA
as the material that communicated this genetic information. Horizontal genetic transfer was then described in Seattle in 1951, in a paper demonstrating that the transfer of a viral gene into ''
Corynebacterium diphtheriae ''Corynebacterium diphtheriae'' is the pathogenic bacterium that causes diphtheria. It is also known as the Klebs-Löffler bacillus, because it was discovered in 1884 by German Bacteriology, bacteriologists Edwin Klebs (1834–1912) and Fried ...

Corynebacterium diphtheriae
'' created a virulent strain from a non-virulent strain, also simultaneously solving the riddle of
diphtheria Diphtheria is an infection caused by the bacteria, bacterium ''Corynebacterium diphtheriae''. Most infections are asymptomatic or have a mild Course (medicine), clinical course, but in some outbreaks more than 10% of those diagnosed with the di ...

diphtheria
(that patients could be infected with the bacteria but not have any symptoms, and then suddenly convert later or never), and giving the first example for the relevance of the
lysogenic cycle Lysogenic cycle, compared to lytic cycle Lysogeny, or the lysogenic cycle, is one of two cycles of viral reproduction (the lytic cycle 300px, Lytic cycle, compared to lysogenic cycleThe lytic cycle ( ) is one of the two cycles of viral repr ...
. Inter-bacterial gene transfer was first described in Japan in a 1959 publication that demonstrated the transfer of antibiotic resistance between different species of
bacteria Bacteria (; common noun bacteria, singular bacterium) are ubiquitous, mostly free-living organisms often consisting of one Cell (biology), biological cell. They constitute a large domain (biology), domain of prokaryotic microorganisms. Typ ...

bacteria
. In the mid-1980s, Syvanen predicted that lateral gene transfer existed, had biological significance, and was involved in shaping evolutionary history from the beginning of life on Earth. As Jian, Rivera and Lake (1999) put it: "Increasingly, studies of genes and genomes are indicating that considerable horizontal transfer has occurred between
prokaryote A prokaryote () is a single-celled organism A unicellular organism, also known as a single-celled organism, is an organism In biology, an organism (from Ancient Greek, Greek: ὀργανισμός, ''organismos'') is any individual contig ...
s" (see also Lake and Rivera, 2007). The phenomenon appears to have had some significance for unicellular
eukaryote Eukaryotes () are organism In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interact ...

eukaryote
s as well. As Bapteste et al. (2005) observe, "additional evidence suggests that gene transfer might also be an important evolutionary mechanism in
protist A protist () is any (that is, an organism whose contain a ) that is not an , , or . While it is likely that protists share a (the ), the exclusion of other eukaryotes means that protists do not form a natural group, or . Therefore, some pro ...
evolution." Grafting of one plant to another can transfer
chloroplast A chloroplast is a type of membrane-bound organelle In cell biology, an organelle is a specialized subunit, usually within a cell (biology), cell, that has a specific function. The name ''organelle'' comes from the idea that these structure ...

chloroplast
s (
organelle In cell biology Cell biology (also cellular biology or cytology) is a branch of biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, ...
s in plant cells that conduct
photosynthesis Photosynthesis is a process used by plants and other organisms to convert Conversion or convert may refer to: Arts, entertainment, and media * Conversion (Doctor Who audio), "Conversion" (''Doctor Who'' audio), an episode of the audio drama ' ...

photosynthesis
),
mitochondrial DNA Mitochondrial DNA (mtDNA or mDNA) is the DNA Deoxyribonucleic acid (; DNA) is a molecule File:Pentacene on Ni(111) STM.jpg, A scanning tunneling microscopy image of pentacene molecules, which consist of linear chains of five car ...

mitochondrial DNA
, and the entire
cell nucleus In cell biology, the nucleus (pl. ''nuclei''; from Latin or , meaning ''kernel'' or ''seed'') is a biological membrane#Function, membrane-bound organelle found in eukaryote, eukaryotic cell (biology), cells. Eukaryotes usually have a single n ...

cell nucleus
containing the
genome In the fields of molecular biology Molecular biology is the branch of biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, M ...

genome
to potentially make a new species. Some
Lepidoptera Lepidoptera ( ; ) is an order Order or ORDER or Orders may refer to: * Orderliness Orderliness is associated with other qualities such as cleanliness Cleanliness is both the abstract state of being clean and free from germs, dirt, trash, or ...

Lepidoptera
(e.g.
monarch butterflies The monarch butterfly or simply monarch (''Danaus plexippus'') is a milkweed butterfly (subfamily Danainae) in the family Nymphalidae. Other common names, depending on region, include milkweed, common tiger, wanderer, and black-veined brown. It ...

monarch butterflies
and
silkworm ''Bombyx mori'', the domestic silk moth, is an insect from the moth Moths are a paraphyletic In taxonomy, a group is paraphyletic if it consists of the group's last common ancestor and all descendants of that ancestor excluding a ...

silkworm
s) have been genetically modified by horizontal gene transfer from the wasp
bracovirus ''Bracovirus'' is a genus of viruses, in the family '' Polydnaviridae''. Bracoviruses are an ancient symbiotic virus contained in parasitic braconid wasps that evolved off of the '' nudivirus'' about 190 million years ago and has been evolving ...
. Bites from insects in the family
Reduviidae The Reduviidae are a large cosmopolitan family of the order Hemiptera Hemiptera (Latin Latin (, or , ) is a classical language belonging to the Italic languages, Italic branch of the Indo-European languages. Latin was originally spoken i ...

Reduviidae
(assassin bugs) can, via a parasite, infect humans with the
trypanosoma ''Trypanosoma'' is a genus Genus /ˈdʒiː.nəs/ (plural genera /ˈdʒen.ər.ə/) is a taxonomic rank In biological classification In biology Biology is the natural science that studies life and living organisms, including th ...

trypanosoma
l
Chagas disease Chagas disease, also known as American trypanosomiasis, is a tropical disease, tropical parasitic disease caused by ''Trypanosoma cruzi''. It is spread mostly by insects known as ''Triatominae'', or "kissing bugs". The symptoms change over the ...
, which can insert its DNA into the human genome. It has been suggested that lateral gene transfer to humans from bacteria may play a role in cancer. Aaron Richardson and Jeffrey D. Palmer state: "Horizontal gene transfer (HGT) has played a major role in bacterial evolution and is fairly common in certain unicellular eukaryotes. However, the prevalence and importance of HGT in the evolution of
multicellular A multicellular organism is an organism In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular ...

multicellular
eukaryotes remain unclear." Due to the increasing amount of evidence suggesting the importance of these phenomena for evolution (see
below Below may refer to: *Earth *Ground (disambiguation) *Soil *Floor *Bottom (disambiguation) *Less than *Temperatures below freezing *Hell or underworld People with the surname *Fred Below (1926–1988), American blues drummer *Fritz von Below (1853 ...
) molecular biologists such as Peter Gogarten have described horizontal gene transfer as "A New Paradigm for Biology".


Mechanisms

There are several mechanisms for horizontal gene transfer: *
Transformation Transformation may refer to: Science and mathematics In biology and medicine * Metamorphosis, the biological process of changing physical form after birth or hatching * Malignant transformation, the process of cells becoming cancerous * Transf ...
, the genetic alteration of a cell resulting from the introduction, uptake and of foreign genetic material (
DNA Deoxyribonucleic acid (; DNA) is a molecule File:Pentacene on Ni(111) STM.jpg, A scanning tunneling microscopy image of pentacene molecules, which consist of linear chains of five carbon rings. A molecule is an electrically neutral gro ...

DNA
or
RNA Ribonucleic acid (RNA) is a polymer A polymer (; Greek ''wikt:poly-, poly-'', "many" + ''wikt:-mer, -mer'', "part") is a Chemical substance, substance or material consisting of very large molecules, or macromolecules, composed of many Re ...

RNA
).Stearns, S. C., & Hoekstra, R. F. (2005). Evolution: An introduction (2nd ed.). Oxford, NY: Oxford Univ. Press. pp. 38-40. This process is relatively common in bacteria, but less so in eukaryotes. Transformation is often used in laboratories to insert novel genes into bacteria for experiments or for industrial or medical applications. See also
molecular biology Molecular biology is the branch of biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactions, P ...
and
biotechnology Biotechnology is a broad area of biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactions, Phy ...

biotechnology
. *, the process in which bacterial DNA is moved from one bacterium to another by a virus (a bacteriophage, or
phage A bacteriophage (), also known informally as a ''phage'' (), is a virus A virus is a that only inside the living of an . Viruses infect all , from animals and plants to s, including and . Since 's 1892 article describing a non-b ...

phage
). *
Bacterial conjugation Bacterial conjugation is the transfer of genetic material between bacterial cells by direct cell-to-cell contact or by a bridge-like connection between two cells. This takes place through a pilus A pilus (Latin Latin (, or , ) is a class ...
, a process that involves the transfer of DNA via a plasmid from a donor cell to a recombinant recipient cell during cell-to-cell contact. * Gene transfer agents, virus-like elements encoded by the host that are found in the
alphaproteobacteria Alphaproteobacteria is a Class (biology), class of bacteria in the phylum Proteobacteria (See also bacterial taxonomy). Its members are highly diverse and possess few commonalities, but nevertheless share a common ancestor. Like all ''Proteobacter ...
order
Rhodobacterales Rhodobacterales are an order (biology), order of the Alphaproteobacteria. Gene transfer agents are viruslike elements produced by Rhodobacterales which transfer DNA and may be an important factor in their evolution. Etymology From Greek ''rhodo ...
.


Horizontal transposon transfer

A
transposable element A transposable element (TE, transposon, or jumping gene) is a DNA sequence DNA sequencing is the process of determining the nucleic acid sequence A nucleic acid sequence is a succession of bases signified by a series of a set of five diff ...
(TE) (also called a transposon or jumping gene) is a mobile segment of DNA that can sometimes pick up a resistance gene and insert it into a plasmid or chromosome, thereby inducing horizontal gene transfer of antibiotic resistance. Horizontal transposon transfer (HTT) refers to the passage of pieces of DNA that are characterized by their ability to move from one
locus Locus (plural loci) is Latin for "place". It may refer to: Entertainment * Locus (comics), a Marvel Comics mutant villainess, a member of the Mutant Liberation Front * Locus (magazine), ''Locus'' (magazine), science fiction and fantasy magazine ...
to another between genomes by means other than parent-to-offspring inheritance. Horizontal gene transfer has long been thought to be crucial to prokaryotic evolution, but there is a growing amount of data showing that HTT is a common and widespread phenomenon in
eukaryote Eukaryotes () are organism In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interact ...

eukaryote
evolution as well. On the transposable element side, spreading between genomes via horizontal transfer may be viewed as a strategy to escape purging due to purifying selection, mutational decay and/or host defense mechanisms. HTT can occur with any type of transposable elements, but
DNA transposon DNA transposons are DNA sequences, sometimes referred to "jumping genes", that can move and integrate to different locations within the genome. They are class II transposable elements (TEs) that move through a DNA intermediate, as opposed to class I ...

DNA transposon
s and LTR retroelements are more likely to be capable of HTT because both have a stable, double-stranded DNA intermediate that is thought to be sturdier than the single-stranded RNA intermediate of non-LTR retroelements, which can be highly degradable. Non-autonomous elements may be less likely to transfer horizontally compared to autonomous elements because they do not encode the proteins required for their own mobilization. The structure of these non-autonomous elements generally consists of an intronless gene encoding a
transposase Transposase is an enzyme Enzymes () are protein Proteins are large s and s that comprise one or more long chains of . Proteins perform a vast array of functions within organisms, including , , , providing and , and from one location ...
protein, and may or may not have a promoter sequence. Those that do not have promoter sequences encoded within the mobile region rely on adjacent host promoters for expression. Horizontal transfer is thought to play an important role in the TE life cycle. HTT has been shown to occur between species and across continents in both plants and animals (Ivancevic et al. 2013), though some TEs have been shown to more successfully colonize the genomes of certain species over others. Both spatial and taxonomic proximity of species has been proposed to favor HTTs in plants and animals. It is unknown how the density of a population may affect the rate of HTT events within a population, but close proximity due to
parasitism Parasitism is a close relationship between species In biology, a species is the basic unit of biological classification, classification and a taxonomic rank of an organism, as well as a unit of biodiversity. A species is often defined ...

parasitism
and cross contamination due to crowding have been proposed to favor HTT in both plants and animals. Successful transfer of a transposable element requires delivery of DNA from donor to host cell (and to the germ line for multi-cellular organisms), followed by integration into the recipient host genome. Though the actual mechanism for the transportation of TEs from donor cells to host cells is unknown, it is established that
naked DNA The structure of part of a DNA double helix Deoxyribonucleic acid (; DNA) is a molecule File:Pentacene on Ni(111) STM.jpg, A scanning tunneling microscopy image of pentacene molecules, which consist of linear chains of five carbon rings ...
and RNA can circulate in bodily fluid. Many proposed vectors include arthropods, viruses, freshwater snails (Ivancevic et al. 2013), endosymbiotic bacteria, and intracellular parasitic bacteria. In some cases, even TEs facilitate transport for other TEs. The arrival of a new TE in a host genome can have detrimental consequences because TE mobility may induce mutation. However, HTT can also be beneficial by introducing new genetic material into a genome and promoting the shuffling of genes and TE domains among hosts, which can be co-opted by the host genome to perform new functions. Moreover, transposition activity increases the TE copy number and generates
chromosomal rearrangementIn genetics Genetics is a branch of biology concerned with the study of genes, genetic variation, and heredity in organisms.Hartl D, Jones E (2005) Though heredity had been observed for millennia, Gregor Mendel, Moravia, Moravian scientist and ...
hotspots. HTT detection is a difficult task because it is an ongoing phenomenon that is constantly changing in frequency of occurrence and composition of TEs inside host genomes. Furthermore, few species have been analyzed for HTT, making it difficult to establish patterns of HTT events between species. These issues can lead to the underestimation or overestimation of HTT events between ancestral and current eukaryotic species.


Methods of detection

Horizontal gene transfer is typically inferred using
bioinformatics Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biology, biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformat ...

bioinformatics
methods, either by identifying atypical sequence signatures ("parametric" methods) or by identifying strong discrepancies between the evolutionary history of particular sequences compared to that of their hosts. The transferred gene ( xenolog) found in the receiving species is more closely related to the genes of the donor species than would be expected.


Viruses

The
virus A virus is a submicroscopic infectious agent In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecu ...

virus
called ''
Mimivirus ''Mimivirus'' is a genus of giant virus A giant virus, sometimes referred to as a girus, is a very large virus A virus is a submicroscopic infectious agent that Viral replication, replicates only inside the living Cell (biology), c ...

Mimivirus
'' infects
amoebae An amoeba (; less commonly spelt ameba or amœba; plural ''am(o)ebas'' or ''am(o)ebae'' ), often called an amoeboid, is a type of cell or unicellular organism A unicellular organism, also known as a single-celled organism, is an organism ...
. Another virus, called ''
Sputnik Sputnik 1 (; see § Etymology) was the first artificial Earth satellite. It was launched into an elliptical low Earth orbit A low Earth orbit (LEO) is an Earth-centered orbit near the planet, often specified as having a period Period may ...
'', also infects amoebae, but it cannot reproduce unless mimivirus has already infected the same cell. "Sputnik's
genome In the fields of molecular biology Molecular biology is the branch of biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, M ...

genome
reveals further insight into its biology. Although 13 of its genes show little similarity to any other known genes, three are closely related to mimivirus and
mamavirus Mamavirus is a large and complex viruses, virus in the DNA virus#Group I: dsDNA viruses, Group I family ''Mimiviridae''. The virus is exceptionally large, and larger than many bacteria. Mamavirus and other mimiviridae belong to nucleocytoplasmic l ...
genes, perhaps cannibalized by the tiny virus as it packaged up particles sometime in its history. This suggests that the
satellite virus A satellite is a subviral agent that depends on the coinfection of a host cell with a helper virus for its replication. Satellites can be divided into two major classes: satellite viruses and satellite nucleic acids. Satellite virus A ...
could perform horizontal gene transfer between viruses, paralleling the way that bacteriophages ferry genes between bacteria." Horizontal transfer is also seen between geminiviruses and tobacco plants.


Prokaryotes

Horizontal gene transfer is common among bacteria, even among very distantly related ones. This process is thought to be a significant cause of increased
drug resistance Drug resistance is the reduction in effectiveness of a medication such as an antimicrobial An antimicrobial is an agent that kills microorganism A microorganism, or microbe,, ''mikros'', "small") and ''organism In biology, an or ...
when one bacterial cell acquires resistance, and the resistance genes are transferred to other species. Transposition and horizontal gene transfer, along with strong natural selective forces have led to multi-drug resistant strains of '' S. aureus'' and many other pathogenic bacteria. Horizontal gene transfer also plays a role in the spread of virulence factors, such as
exotoxin An exotoxin is a toxin A toxin is a harmful substance produced within living cells or organisms; synthetic toxicants created by artificial processes are thus excluded. The term was first used by organic chemist Ludwig Brieger (1849–1919), de ...
s and exoenzymes, amongst bacteria. A prime example concerning the spread of exotoxins is the adaptive evolution of
Shiga toxin Shiga toxins are a family of related toxins A toxin is a harmful substance produced within living cells or organisms; synthetic toxicants created by artificial processes are thus excluded. The term was first used by organic chemist Ludwi ...
s in ''E. coli'' through horizontal gene transfer via transduction with ''
Shigella ''Shigella'' is a genus Genus (plural genera) is a taxonomic rank Taxonomy (general) is the practice and science of classification of things or concepts, including the principles that underlie such classification. The term may also refer to ...
'' species of bacteria. Strategies to combat certain bacterial infections by targeting these specific virulence factors and mobile genetic elements have been proposed. For example, horizontally transferred genetic elements play important roles in the virulence of ''
E. coli ''Escherichia coli'' (),Wells, J. C. (2000) Longman Pronunciation Dictionary. Harlow ngland Pearson Education Ltd. also known as ''E. coli'' (), is a Gram-negative Gram-negative bacteria are bacteria Bacteria (; common noun bacteri ...

E. coli
'', ''
Salmonella ''Salmonella'' is a genus Genus /ˈdʒiː.nəs/ (plural genera /ˈdʒen.ər.ə/) is a taxonomic rank In biological classification In biology, taxonomy () is the scientific study of naming, defining (Circumscription (taxonomy), circ ...
'', ''
Streptococcus ''Streptococcus'' is a genus Genus /ˈdʒiː.nəs/ (plural genera /ˈdʒen.ər.ə/) is a taxonomic rank In biological classification In biology, taxonomy () is the scientific study of naming, defining (Circumscription (taxonomy), ...

Streptococcus
'' and ''
Clostridium perfringens ''Clostridium perfringens'' (formerly known as ''C. welchii'', or ''Bacillus welchii'') is a Gram-positive In bacteriology, gram-positive bacteria are bacteria that give a positive result in the Gram stain test, which is traditionally used to ...

Clostridium perfringens
''. In prokaryotes, restriction-modification systems are known to provide immunity against horizontal gene transfer and in stabilizing mobile genetic elements. Genes encoding restriction modification systems have been reported to move between prokaryotic genomes within
mobile genetic elements Mobile genetic elements (MGEs) sometimes called selfish genetic elements are a type of genetic material Nucleic acids are biopolymer Biopolymers are natural polymer A polymer (; Greek ''poly- Poly, from the Greek :wikt:πολύς, πο ...
(MGE) such as
plasmid A plasmid is a small, extrachromosomal DNA Extrachromosomal DNA (abbreviated ecDNA) is any DNA that is found off the chromosome A chromosome is a long DNA molecule with part or all of the genetic material of an organism. Most eukaryo ...
s,
prophage A prophage is a bacteriophage A bacteriophage (), also known informally as a ''phage'' (), is a virus A virus is a that only inside the living of an . Viruses infect all , from animals and plants to s, including and . Since 's 1 ...
s, insertion sequences/transposons, integrative conjugative elements (ICE), and
integron Integrons are genetic mechanisms that allow bacteria to adapt and evolve rapidly through the stockpiling and expression of new genes. These genes are embedded in a specific genetic structure called gene cassette In biology, a gene (from ''geno ...

integron
s. Still, they are more frequently a chromosomal-encoded barrier to MGE than an MGE-encoded tool for cell infection. Lateral gene transfer via a mobile genetic element, namely the integrated conjugative element (ICE) ''Bs1'' has been reported for its role in the global DNA damage SOS response of the gram positive ''Bacillus subtilis''. Furthermore it has been linked with the radiation and desiccation resistance of ''Bacillus pumilus'' SAFR-032 spores, isolated from spacecraft cleanroom facilities. Transposon insertion elements have been reported to increase the fitness of gram-negative ''
E. coli ''Escherichia coli'' (),Wells, J. C. (2000) Longman Pronunciation Dictionary. Harlow ngland Pearson Education Ltd. also known as ''E. coli'' (), is a Gram-negative Gram-negative bacteria are bacteria Bacteria (; common noun bacteri ...

E. coli
'' strains through either major transpositions or genome rearrangements, and increasing mutation rates. In a study on the effects of long-term exposure of simulated microgravity on non-pathogenic ''E. coli'', the results showed transposon insertions occur at loci, linked to SOS stress response. When the same ''E. coli'' strain was exposed to a combination of simulated microgravity and trace (background) levels of (the broad spectrum) antibiotic (
chloramphenicol Chloramphenicol is an antibiotic An antibiotic is a type of antimicrobial substance active against bacteria. It is the most important type of antibacterial agent for fighting pathogenic bacteria, bacterial infections, and antibiotic medicat ...

chloramphenicol
), the results showed transposon-mediated rearrangements (TMRs), disrupting genes involved in bacterial adhesion, and deleting an entire segment of several genes involved with motility and chemotaxis. Both these studies have implications for microbial growth, adaptation to and antibiotic resistance in real time space conditions.


Bacterial transformation

Natural transformation In category theory Category theory formalizes mathematical structure In mathematics Mathematics (from Ancient Greek, Greek: ) includes the study of such topics as quantity (number theory), mathematical structure, structure (algebra), s ...
is a bacterial adaptation for DNA transfer (HGT) that depends on the expression of numerous bacterial genes whose products are responsible for this process. In general, transformation is a complex, energy-requiring developmental process. In order for a bacterium to bind, take up and recombine exogenous DNA into its chromosome, it must become competent, that is, enter a special physiological state. Competence development in ''
Bacillus subtilis ''Bacillus subtilis'', known also as the hay bacillus or grass bacillus, is a Gram-positive In bacteriology Bacteriology is the branch and specialty of biology Biology is the natural science that studies life and living organisms, incl ...

Bacillus subtilis
'' requires expression of about 40 genes. The DNA integrated into the host chromosome is usually (but with infrequent exceptions) derived from another bacterium of the same
species In biology, a species is the basic unit of biological classification, classification and a taxonomic rank of an organism, as well as a unit of biodiversity. A species is often defined as the largest group of organisms in which any two individu ...

species
, and is thus homologous to the resident chromosome. The capacity for natural transformation occurs in at least 67 prokaryotic species. Competence for transformation is typically induced by high cell density and/or nutritional limitation, conditions associated with the of bacterial growth. Competence appears to be an adaptation for DNA repair. Transformation in bacteria can be viewed as a primitive sexual process, since it involves interaction of homologous DNA from two individuals to form recombinant DNA that is passed on to succeeding generations. Although transduction is the form of HGT most commonly associated with
bacteriophage A bacteriophage (), also known informally as a ''phage'' (), is a virus A virus is a that only inside the living of an . Viruses infect all , from animals and plants to s, including and . Since 's 1892 article describing a non-b ...

bacteriophage
s, certain phages may also be able to promote transformation.


Bacterial conjugation

Conjugation Conjugation or conjugate may refer to: Linguistics * Grammatical conjugation, the modification of a verb from its basic form * Emotive conjugation or Russell's conjugation, the use of loaded language Mathematics * Complex conjugation, the change ...
in ''
Mycobacterium smegmatis ''Mycobacterium smegmatis'' is an acid-fast 320px, ''Mycobacterium tuberculosis'' (stained red) in tissue (blue). Acid-fastness is a physical property of certain bacterial and Eukaryote, eukaryotic cells, as well as some sub-cellular structures, ...

Mycobacterium smegmatis
'', like conjugation in ''
E. coli ''Escherichia coli'' (),Wells, J. C. (2000) Longman Pronunciation Dictionary. Harlow ngland Pearson Education Ltd. also known as ''E. coli'' (), is a Gram-negative Gram-negative bacteria are bacteria Bacteria (; common noun bacteri ...

E. coli
'', requires stable and extended contact between a donor and a recipient strain, is DNase resistant, and the transferred DNA is incorporated into the recipient chromosome by
homologous recombination Homologous recombination is a type of genetic recombination in which genetic information is exchanged between two similar or identical molecules of double-stranded or single-stranded nucleic acids (usually DNA as in Cell (biology), cellular organi ...

homologous recombination
. However, unlike ''E. coli'' (Hfr), mycobacterial conjugation is a type of HGT that is chromosome rather than plasmid based. Furthermore, in contrast to ''E. coli'' (Hfr) conjugation, in ''M. smegmatis'' all regions of the chromosome are transferred with comparable efficiencies. Substantial blending of the parental genomes was found as a result of conjugation, and this blending was regarded as reminiscent of that seen in the meiotic products of sexual reproduction.


Archaeal DNA transfer

The
archaeon Archaea ( ; singular archaeon ) constitute a domain Domain may refer to: Mathematics *Domain of a function, the set of input values for which the (total) function is defined **Domain of definition of a partial function **Natural domain of a pa ...

archaeon
''
Sulfolobus solfataricus ''Saccharolobus solfataricus'' is a species In biology, a species is the basic unit of biological classification, classification and a taxonomic rank of an organism, as well as a unit of biodiversity. A species is often defined as the large ...
'', when irradiated, strongly induces the formation of
type IV pili A pilus (Latin Latin (, or , ) is a classical language belonging to the Italic branch of the Indo-European languages. Latin was originally spoken in the area around Rome, known as Latium. Through the power of the Roman Republic, it bec ...
which then facilitates cellular aggregation. Exposure to chemical agents that cause DNA damage also induces cellular aggregation. Other physical stressors, such as temperature shift or pH, do not induce aggregation, suggesting that DNA damage is a specific inducer of cellular aggregation. UV-induced cellular aggregation mediates intercellular chromosomal HGT marker exchange with high frequency, and UV-induced cultures display recombination rates that exceed those of uninduced cultures by as much as three orders of magnitude. ''S. solfataricus'' cells aggregate preferentially with other cells of their own species. Frols et al. and Ajon et al. suggested that UV-inducible DNA transfer is likely an important mechanism for providing increased repair of damaged DNA via homologous recombination. This process can be regarded as a simple form of sexual interaction. Another thermophilic species, ''
Sulfolobus acidocaldarius ''Sulfolobus acidocaldarius'' is a thermoacidophilic archaeon that belongs to the kingdom Crenarchaeota. ''S. acidocaldarius'' was the first ''Sulfolobus'' species to be described, in 1972 by Thomas D. Brock and collaborators. This species was fo ...
'', is able to undergo HGT. ''S. acidocaldarius'' can exchange and recombine chromosomal markers at temperatures up to 84 °C. UV exposure induces pili formation and cellular aggregation. Cells with the ability to aggregate have greater survival than mutants lacking pili that are unable to aggregate. The frequency of recombination is increased by DNA damage induced by UV-irradiation and by DNA damaging chemicals. The ''ups'' operon, containing five genes, is highly induced by UV irradiation. The proteins encoded by the ''ups'' operon are employed in UV-induced pili assembly and cellular aggregation leading to intercellular DNA exchange and
homologous recombination Homologous recombination is a type of genetic recombination in which genetic information is exchanged between two similar or identical molecules of double-stranded or single-stranded nucleic acids (usually DNA as in Cell (biology), cellular organi ...

homologous recombination
. Since this system increases the fitness of ''S. acidocaldarius'' cells after UV exposure, Wolferen et al. considered that transfer of DNA likely takes place in order to repair UV-induced DNA damages by homologous recombination.


Eukaryotes

"Sequence comparisons suggest recent horizontal transfer of many genes among diverse species including across the boundaries of
phylogenetic In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactions, Physiology, physiological mechanism ...

phylogenetic
'domains'. Thus determining the phylogenetic history of a species can not be done conclusively by determining evolutionary trees for single genes."


Organelle to nuclear genome

*Analysis of
DNA sequence DNA sequencing is the process of determining the nucleic acid sequence A nucleic acid sequence is a succession of bases signified by a series of a set of five different letters that indicate the order of nucleotides Nucleotides are organic ...

DNA sequence
s suggests that horizontal gene transfer has occurred within eukaryotes from the chloroplast and
mitochondrial genome Mitochondrial DNA (mtDNA or mDNA) is the DNA located in mitochondrion, mitochondria, cellular organelles within eukaryotic cells that convert chemical energy from food into a form that cells can use, such as adenosine triphosphate (ATP). Mi ...
s to the
nuclear genome Nuclear DNA (nDNA), or nuclear deoxyribonucleic acid, is the DNA Deoxyribonucleic acid (; DNA) is a molecule File:Pentacene on Ni(111) STM.jpg, A scanning tunneling microscopy image of pentacene molecules, which consist of linear chain ...
. As stated in the
endosymbiotic theory Symbiogenesis, endosymbiotic theory, or serial endosymbiotic theory, is the leading evolutionary theory of the origin of eukaryotic Eukaryotes () are organism In biology, an organism () is any organic, life, living system that fun ...

endosymbiotic theory
,
chloroplast A chloroplast is a type of membrane-bound organelle In cell biology, an organelle is a specialized subunit, usually within a cell (biology), cell, that has a specific function. The name ''organelle'' comes from the idea that these structure ...

chloroplast
s and
mitochondria A mitochondrion (; ) is a double-membrane A membrane is a selective barrier; it allows some things to pass through but stops others. Such things may be molecules, ions, or other small particles. Biological membranes include cell membranes ...

mitochondria
probably originated as bacterial
endosymbiont An endosymbiont or endobiont is any organism In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, mol ...
s of a progenitor to the eukaryotic cell.


Organelle to organelle

*
Mitochondrial gene Electron microscopy reveals mitochondrial DNA in discrete foci. Bars: 200 nm. (A) Cytoplasmic section after immunogold labelling with anti-DNA; gold particles marking mtDNA are found near the mitochondrial membrane (black dots in upper right). ...
s moved to parasites of the
Rafflesiaceae Illustration of ''Rhizanthes'' (then known as ''Brugmansia''), a Rafflesiaceae species from ''Der Bau und die Eigenschaften der Pflanzen'' (1913). The Rafflesiaceae are a family of rare parasitic Parasitism is a Symbiosis, symbiotic biolog ...
plant family from their hosts and from chloroplasts of a still-unidentified plant to the mitochondria of the bean ''
Phaseolus ''Phaseolus'' (bean, wild bean) is a genus of herbaceous to woody annual and perennial vines in the family (biology), family Fabaceae containing about 70 plant species, all native to the Americas, primarily Mesoamerica. It is one of the most eco ...
''.


Viruses to plants

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


Bacteria to fungi

*Horizontal transfer occurs from bacteria to some
fungi A fungus (plural The plural (sometimes abbreviated An abbreviation (from Latin ''brevis'', meaning ''short'') is a shortened form of a word or phrase, by any method. It may consist of a group of letters, or words taken from the full ...

fungi
, such as the yeast ''
Saccharomyces cerevisiae ''Saccharomyces cerevisiae'' () is a species of yeast Yeasts are eukaryotic Eukaryotes () are organism In biology, an organism () is any organic, life, living system that functions as an individual entity. All organisms are ...

Saccharomyces cerevisiae
''.


Bacteria to plants

* Agrobacterium, a pathogenic bacterium that causes cells to proliferate as crown galls and proliferating roots is an example of a bacterium that can transfer genes to plants and this plays an important role in plant evolution.


Bacteria to insects

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


Bacteria to animals

*Bdelloid rotifers currently hold the 'record' for HGT in animals with ~8% of their genes from bacterial origins. Tardigrades were thought to break the record with 17.5% HGT, but that finding was an artifact of bacterial contamination. *A study found the genomes of 40 animals (including 10 primates, four ''Caenorhabditis'' worms, and 12 ''Drosophila'' insects) contained genes which the researchers concluded had been transferred from bacteria and fungi by horizontal gene transfer. The researchers estimated that for some nematodes and Drosophila insects these genes had been acquired relatively recently. *A bacteriophage-mediated mechanism transfers genes between prokaryotes and eukaryotes. Nuclear localization signals in bacteriophage terminal proteins (TP) prime DNA replication and become covalently linked to the viral genome. The role of virus and bacteriophages in HGT in bacteria, suggests that TP-containing genomes could be a vehicle of inter-kingdom genetic information transference all throughout evolution.


Endosymbiont to insects and nematodes

*The Callosobruchus chinensis, adzuki bean beetle has acquired genetic material from its (non-beneficial) endosymbiont ''Wolbachia''. New examples have recently been reported demonstrating that Wolbachia bacteria represent an important potential source of genetic material in arthropods and filarial nematodes, filarial nematodes.


Plant to plant

*''Striga hermonthica'', a parasitic eudicot, has received a gene from sorghum (''Sorghum bicolor'') to its nuclear genome. The gene's functionality is unknown. *A gene that allowed ferns to survive in dark forests came from the hornwort, which grows in mats on streambanks or trees. The neochrome gene arrived about 180 million years ago.


Plants to animals

*The eastern emerald sea slug ''Elysia chlorotica'' has been suggested by fluorescence in situ hybridization (FISH) analysis to contain photosynthesis-supporting genes obtained from an algae (''Vaucheria litorea)'' in their diet. LGT in Sacoglossa is now thought to be an artifact and no trace of LGT was found upon sequencing the genome of ''Elysia chlorotica''.


Plant to fungus

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


Fungi to insects

*Pea aphids (''Acyrthosiphon pisum'') contain multiple genes from fungus, fungi. Plants, fungi, and microorganisms can synthesize carotenoids, but torulene made by pea aphids is the only carotenoid known to be synthesized by an organism in the animal kingdom.


Animals to animals

* Smelt (fish), Smelt fish received antifreeze protein (AFP) gene from herring through a direct horizontal transfer.


Human to protozoan

*The malaria pathogen ''Plasmodium vivax'' acquired genetic material from humans that might help facilitate its long stay in the body.


Human genome

*One study identified approximately 100 of humans' approximately 20,000 total genes which likely resulted from horizontal gene transfer, but this number has been challenged by several researchers arguing these candidate genes for HGT are more likely the result of gene loss combined with differences in the rate of evolution.


Artificial horizontal gene transfer

Genetic engineering is essentially horizontal gene transfer, albeit with synthetic expression cassettes. The Sleeping Beauty transposon system (SB) was developed as a synthetic gene transfer agent that was based on the known abilities of Tc1/mariner transposons to invade genomes of extremely diverse species. The SB system has been used to introduce genetic sequences into a wide variety of animal genomes.


Importance in evolution

Horizontal gene transfer is a potential Lurking variable, confounding factor in inferring phylogenetic trees based on the sequence of one gene.Graham Lawton
Why Darwin was wrong about the tree of life
' New Scientist Magazine issue 2692 21 January 2009 Accessed February 2009
For example, given two distantly related bacteria that have exchanged a gene a phylogenetic tree including those species will show them to be closely related because that gene is the same even though most other genes are dissimilar. For this reason, it is often ideal to use other information to infer robust phylogenies such as the presence or absence of genes or, more commonly, to include as wide a range of genes for phylogenetic analysis as possible. For example, the most common gene to be used for constructing phylogenetic relationships in
prokaryote A prokaryote () is a single-celled organism A unicellular organism, also known as a single-celled organism, is an organism In biology, an organism (from Ancient Greek, Greek: ὀργανισμός, ''organismos'') is any individual contig ...
s is the 16S ribosomal RNA gene since its sequences tend to be conserved among members with close phylogenetic distances, but variable enough that differences can be measured. However, in recent years it has also been argued that 16s rRNA genes can also be horizontally transferred. Although this may be infrequent, the validity of 16s rRNA-constructed phylogenetic trees must be reevaluated. Biologist Johann Peter Gogarten suggests "the original metaphor of a tree no longer fits the data from recent genome research" therefore "biologists should use the metaphor of a mosaic to describe the different histories combined in individual genomes and use the metaphor of a net to visualize the rich exchange and cooperative effects of HGT among microbes". There exist several methods to infer such phylogenetic networks. Using single genes as phylogenetic markers, it is difficult to trace organismal phylogeny in the presence of horizontal gene transfer. Combining the simple coalescent theory, coalescence model of cladogenesis with rare HGT horizontal gene transfer events suggest there was no single most recent common ancestor that contained all of the genes ancestral to those shared among the three domains of life. Each contemporary molecule has its own history and traces back to an individual molecule cenancestor. However, these molecular ancestors were likely to be present in different organisms at different times."


Challenge to the tree of life

Horizontal gene transfer poses a possible challenge to the concept of the last universal common ancestor (LUCA) at the root of the tree of life (science), tree of life first formulated by Carl Woese, which led him to propose the Archaea as a third domain of life. Indeed, it was while examining the new three-domain view of life that horizontal gene transfer arose as a complicating issue: ''Archaeoglobus, Archaeoglobus fulgidus'' was seen as an anomaly with respect to a phylogenetic tree based upon the encoding for the enzyme HMGCoA reductase—the organism in question is a definite Archaean, with all the cell lipids and transcription machinery that are expected of an Archaean, but whose HMGCoA genes are of bacterial origin. Scientists are broadly agreed on symbiogenesis, that mitochondrion, mitochondria in eukaryotes derived from alpha-proteobacterial cells and that
chloroplast A chloroplast is a type of membrane-bound organelle In cell biology, an organelle is a specialized subunit, usually within a cell (biology), cell, that has a specific function. The name ''organelle'' comes from the idea that these structure ...

chloroplast
s came from ingested cyanobacteria, and other gene transfers may have affected early eukaryotes. (In contrast, multicellular eukaryotes have mechanisms to prevent horizontal gene transfer, including separated germ cells.) If there had been continued and extensive gene transfer, there would be a complex network with many ancestors, instead of a tree of life with sharply delineated lineages leading back to a LUCA. However, a LUCA can be identified, so horizontal transfers must have been relatively limited.


Phylogenetic information in HGT

It has been remarked that, despite the complications, the detection of horizontal gene transfers brings valuable phylogenetic and dating information. The potential of HGT to be used for dating phylogenies has recently been confirmed.


The chromosomal organization of horizontal gene transfer

The acquisition of new genes has the potential to disorganize the other genetic elements and hinder the function of the bacterial cell, thus affecting the competitiveness of bacteria. Consequently, bacterial adaptation lies in a conflict between the advantages of acquiring beneficial genes, and the need to maintain the organization of the rest of its genome. Horizontally transferred genes are typically concentrated in only ~1% of the chromosome (in regions called hotspots). This concentration increases with genome size and with the rate of transfer. Hotspots diversify by rapid gene turnover; their chromosomal distribution depends on local contexts (neighboring core genes), and content in mobile genetic elements. Hotspots concentrate most changes in gene repertoires, reduce the trade-off between genome diversification and organization, and should be treasure troves of strain-specific adaptive genes. Most mobile genetic elements and antibiotic resistance genes are in hotspots, but many hotspots lack recognizable mobile genetic elements and exhibit frequent homologous recombination at flanking core genes. Overrepresentation of hotspots with fewer mobile genetic elements in naturally transformable bacteria suggests that homologous recombination and horizontal gene transfer are tightly linked in genome evolution.


Genes

There is evidence for historical horizontal transfer of the following genes: *Lycopene cyclase for carotenoid biosynthesis, between Chlorobi and Cyanobacteria. *''TetO'' gene conferring resistance to tetracycline, between ''Campylobacter jejuni''. *Neochrome, a gene in some ferns that enhances their ability to survive in dim light. Believed to have been acquired from algae sometime during the Cretaceous. *Transfer of a cysteine synthase from a bacterium into herbivore, phytophagous mites and
Lepidoptera Lepidoptera ( ; ) is an order Order or ORDER or Orders may refer to: * Orderliness Orderliness is associated with other qualities such as cleanliness Cleanliness is both the abstract state of being clean and free from germs, dirt, trash, or ...

Lepidoptera
allowing the detoxification of cyanogenic glycosides, cyanogenic glucosides produced by host plants. *The LINE1 sequence has transferred from humans to the gonorrhea bacteria.


See also

*Agrobacterium, a bacterium well known for its ability to transfer DNA between itself and plants. *Endogenous retrovirus *Genetically modified organism *Inferring horizontal gene transfer *Integron *Mobile genetic elements *Phylogenetic network *Phylogenetic tree *Provirus *Reassortment *Retrotransposon *Symbiogenesis *Tree of life (biology) *Xenobiology


References


Further reading

*
– Papers by Dr Michael Syvanen on Horizontal Gene Transfer
* * * This article seeks to shift the emphasis in early phylogenetics, phylogenic adaptation from vertical to horizontal gene transfer. He uses the term "Darwinian Threshold" for the time of major transition of evolutionary mechanisms from mostly horizontal to mostly vertical transfer, and the "origin of speciation". * 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. * * * * * * * * *


External links

*:Citizendium:Horizontal gene transfer *:Citizendium:Horizontal gene transfer in prokaryotes *:Citizendium:Horizontal gene transfer in plants *:Citizendium:Horizontal gene transfer (History) {{DEFAULTSORT:Horizontal Gene Transfer Antimicrobial resistance Genetics Microbial population biology