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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 that consists of a single cell, unlike a multicellular organism that consists of multiple cells. Organisms fall into two general categories: prokaryotic organisms and ...
and/or
multicellular organisms other than by the ("vertical") transmission of
DNA from parent to offspring (
reproduction). HGT is an important factor in the evolution of many organisms.
HGT is influencing scientific understanding of higher order evolution while more significantly shifting perspectives on bacterial evolution.
Horizontal gene transfer is the primary mechanism for the spread of
antibiotic resistance in bacteria,
[ and plays an important role in the evolution of ]bacteria
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. Typically a few micrometr ...
that can degrade novel compounds such as human-created pesticides 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, especially in animal systems, virulence refers to the degree of damage caused by a microbe to its host. The pathogenicity of an organism—its ability to ...
. It often involves temperate
In geography, the temperate climates of Earth occur in the middle latitudes (23.5° to 66.5° N/S of Equator), which span between the tropics and the polar regions of Earth. These zones generally have wider temperature ranges throughout ...
bacteriophages and 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
* Tran ...
, transduction 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 chang ...
, subsequently arming the antibiotic resistant genes' recipient against antibiotics. The rapid spread of antibiotic resistance genes in this manner is becoming a challenge to manage in the field of medicine. Ecological factors may also play a role in the HGT of antibiotic resistant genes.
Horizontal gene transfer is recognized as a pervasive evolutionary process that distributes genes between divergent prokaryotic lineages and can also involve eukaryotes. It is postulated that HGT promotes the maintenance of a universal life biochemistry and, subsequently, the universality of the genetic code.
History
Griffith's experiment
Griffith's experiment, reported in 1928 by Frederick Griffith, was the first experiment suggesting that bacteria are capable of transferring genetic information through a process known as transformation. Griffith's findings were followed by res ...
, reported in 1928 by Frederick Griffith
Frederick Griffith (1877–1941) was a British bacteriologist whose focus was the epidemiology and pathology of bacterial pneumonia. In January 1928 he reported what is now known as Griffith's Experiment, the first widely accepted demonstrati ...
, 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
* Tran ...
. Griffith's findings were followed by research in the late 1930s and early 40s that isolated DNA as the material that communicated this genetic information.
Horizontal genetic transfer was then described in Seattle in 1951, in a paper demonstrating that the transfer of a viral gene into '' Corynebacterium diphtheriae'' created a virulent strain from a non-virulent strain, also simultaneously solving the riddle of diphtheria
Diphtheria is an infection caused by the bacterium '' Corynebacterium diphtheriae''. Most infections are asymptomatic or have a mild clinical course, but in some outbreaks more than 10% of those diagnosed with the disease may die. Signs and s ...
(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
Lysogeny, or the lysogenic cycle, is one of two cycles of viral reproduction (the lytic cycle being the other). Lysogeny is characterized by integration of the bacteriophage nucleic acid into the host bacterium's genome or formation of a circu ...
. 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 (; 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. Typically a few micrometr ...
. In the mid-1980s, Syvanen postulated that biologically significant lateral gene transfer has existed since the beginning of life on Earth and has been involved in shaping all of evolutionary history.
As Jian, Rivera and Lake (1999) put it: "Increasingly, studies of genes and genomes are indicating that considerable horizontal transfer has occurred between prokaryote
A prokaryote () is a single-celled organism that lacks a nucleus and other membrane-bound organelles. The word ''prokaryote'' comes from the Greek πρό (, 'before') and κάρυον (, 'nut' or 'kernel').Campbell, N. "Biology:Concepts & Conne ...
s" (see also Lake and Rivera, 2007). The phenomenon appears to have had some significance for unicellular eukaryotes as well. As Bapteste et al. (2005) observe, "additional evidence suggests that gene transfer might also be an important evolutionary mechanism in protist
A protist () is any eukaryotic organism (that is, an organism whose cells contain a cell nucleus) that is not an animal, plant, or fungus. While it is likely that protists share a common ancestor (the last eukaryotic common ancestor), the exc ...
evolution."
Grafting of one plant to another can transfer chloroplasts ( organelles in plant cells that conduct photosynthesis
Photosynthesis is a process used by plants and other organisms to convert light energy into chemical energy that, through cellular respiration, can later be released to fuel the organism's activities. Some of this chemical energy is stored i ...
), mitochondrial DNA, and the entire cell nucleus containing the genome
In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding g ...
to potentially make a new species. Some 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. ...
and silkworms) 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 at ...
. Bites from insects in the family Reduviidae
The Reduviidae are a large cosmopolitan family of the order Hemiptera (true bugs). Among the Hemiptera and together with the Nabidae almost all species are terrestrial ambush predators: most other predatory Hemiptera are aquatic. The main exampl ...
(assassin bugs) can, via a parasite, infect humans with the trypanosoma
''Trypanosoma'' is a genus of kinetoplastids (class Trypanosomatidae), a monophyletic group of unicellular parasitic flagellate protozoa. Trypanosoma is part of the phylum Sarcomastigophora. The name is derived from the Greek ''trypano-'' ( ...
l Chagas disease, 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 that consists of more than one cell, in contrast to unicellular organism.
All species of animals, land plants and most fungi are multicellular, as are many algae, whereas a few organisms are partially un ...
eukaryotes remain unclear."
Due to the increasing amount of evidence suggesting the importance of these phenomena for evolution (see below) molecular biologists such as Peter Gogarten have described horizontal gene transfer as "A New Paradigm for Biology".
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
* Tran ...
, the genetic alteration of a cell
Cell most often refers to:
* Cell (biology), the functional basic unit of life
Cell may also refer to:
Locations
* Monastic cell, a small room, hut, or cave in which a religious recluse lives, alternatively the small precursor of a monastery ...
resulting from the introduction, uptake and expression
Expression may refer to:
Linguistics
* Expression (linguistics), a word, phrase, or sentence
* Fixed expression, a form of words with a specific meaning
* Idiom, a type of fixed expression
* Metaphorical expression, a particular word, phrase, o ...
of foreign genetic material ( DNA or RNA
Ribonucleic acid (RNA) is a polymeric molecule essential in various biological roles in coding, decoding, regulation and expression of genes. RNA and deoxyribonucleic acid ( DNA) are nucleic acids. Along with lipids, proteins, and carbohydra ...
).[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 that seeks to understand the molecular basis of biological activity in and between cells, including biomolecular synthesis, modification, mechanisms, and interactions. The study of chemical and physi ...
and biotechnology
Biotechnology is the integration of natural sciences and engineering sciences in order to achieve the application of organisms, cells, parts thereof and molecular analogues for products and services. The term ''biotechnology'' was first used ...
.
* Transduction, 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 duplodnaviria virus that infects and replicates within bacteria and archaea. The term was derived from "bacteria" and the Greek φαγεῖν ('), meaning "to devour". Bacter ...
).[
* Bacterial conjugation, a process that involves the transfer of DNA via a plasmid from a donor cell to a recombinant recipient cell during cell-to-cell contact.][
*]Gene transfer agent
Gene transfer agents (GTAs) are DNA-containing virus-like particles that are produced by some bacteria and archaea and mediate horizontal gene transfer. Different GTA types have originated independently from viruses in several bacterial and archae ...
s, virus-like elements encoded by the host that are found in the alphaproteobacteria
Alphaproteobacteria is a class of bacteria in the phylum Pseudomonadota (formerly Proteobacteria). The Magnetococcales and Mariprofundales are considered basal or sister to the Alphaproteobacteria. The Alphaproteobacteria are highly diverse and ...
order Rhodobacterales
Rhodobacterales are an 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 ''rhodon'', the rose
...
.
Horizontal transposon transfer
A transposable element
A transposable element (TE, transposon, or jumping gene) is a nucleic acid sequence in DNA that can change its position within a genome, sometimes creating or reversing mutations and altering the cell's genetic identity and genome size. Transp ...
(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), science fiction and fantasy magazine
** ''Locus Award' ...
to another between genomes by means other than parent-to-offspring inheritance. Horizontal gene transfer has long been thought to be crucial to prokaryotic evolution, but there is a growing amount of data showing that HTT is a common and widespread phenomenon in eukaryote evolution as well. 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 ...
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
A transposase is any of a class of enzymes capable of binding to the end of a transposon and catalysing its movement to another part of a genome, typically by a cut-and-paste mechanism or a replicative mechanism, in a process known as transpositio ...
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 and cross contamination due to crowding have been proposed to favor HTT in both plants and animals. Successful transfer of a transposable element requires delivery of DNA from donor to host cell (and to the germ line for multi-cellular organisms), followed by integration into the recipient host genome. Though the actual mechanism for the transportation of TEs from donor cells to host cells is unknown, it is established that naked DNA and RNA can circulate in bodily fluid. Many proposed vectors include arthropods, viruses, freshwater snails (Ivancevic et al. 2013), endosymbiotic bacteria, and intracellular parasitic bacteria. In some cases, even TEs facilitate transport for other TEs.
The arrival of a new TE in a host genome can have detrimental consequences because TE mobility may induce mutation. However, HTT can also be beneficial by introducing new genetic material into a genome and promoting the shuffling of genes and TE domains among hosts, which can be co-opted by the host genome to perform new functions. Moreover, transposition activity increases the TE copy number and generates chromosomal rearrangement
In genetics, a chromosomal rearrangement is a mutation that is a type of chromosome abnormality involving a change in the structure of the native chromosome. Such changes may involve several different classes of events, like deletions, duplica ...
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 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 that replicates only inside the living cells of an organism. Viruses infect all life forms, from animals and plants to microorganisms, including bacteria and archaea.
Since Dmitri Ivanovsk ...
called ''Mimivirus
''Mimivirus'' is a genus of giant viruses, in the family '' Mimiviridae''. Amoeba serve as their natural hosts. This genus contains a single identified species named ''Acanthamoeba polyphaga mimivirus'' (APMV). It also refers to a group of phyl ...
'' infects amoebae
An amoeba (; less commonly spelled ameba or amœba; plural ''am(o)ebas'' or ''am(o)ebae'' ), often called an amoeboid, is a type of cell or unicellular organism with the ability to alter its shape, primarily by extending and retracting pseudopo ...
. Another virus, called '' Sputnik'', also infects amoebae, but it cannot reproduce unless mimivirus has already infected the same cell. "Sputnik's genome
In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding g ...
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 virus in the Group I family ''Mimiviridae''. The virus is exceptionally large, and larger than many bacteria. Mamavirus and other mimiviridae belong to nucleocytoplasmic large DNA virus (NCLDVs) family. Mamavirus ...
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 viruses, which ar ...
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 or an antineoplastic in treating a disease or condition. The term is used in the context of resistance that pathogens or cancers have "acquired", that is ...
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 exotoxins and ]exoenzyme
An exoenzyme, or extracellular enzyme, is an enzyme that is secreted by a cell and functions outside that cell. Exoenzymes are produced by both prokaryotic and eukaryotic cells and have been shown to be a crucial component of many biological pr ...
s, 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 with two major groups, Stx1 and Stx2, expressed by genes considered to be part of the genome of lambdoid prophages. The toxins are named after Kiyoshi Shiga, who first described the bacterial or ...
s in ''E. coli'' through horizontal gene transfer via transduction with ''Shigella
''Shigella'' is a genus of bacteria that is Gram-negative, facultative anaerobic, non-spore-forming, nonmotile, rod-shaped, and genetically closely related to '' E. coli''. The genus is named after Kiyoshi Shiga, who first discovered it in 1 ...
'' 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'', '' Salmonella'', ''Streptococcus
''Streptococcus'' is a genus of gram-positive ' (plural ) or spherical bacteria that belongs to the family Streptococcaceae, within the order Lactobacillales (lactic acid bacteria), in the phylum Bacillota. Cell division in streptococci occurs ...
'' and ''Clostridium perfringens
''Clostridium perfringens'' (formerly known as ''C. welchii'', or ''Bacillus welchii'') is a Gram-positive, rod-shaped, anaerobic, spore-forming pathogenic bacterium of the genus ''Clostridium''. ''C. perfringens'' is ever-present in nature an ...
''.[
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 that can move around within a genome, or that can be transferred from one species or replicon to another. MGEs are found in all organisms. In ...
(MGE) such as plasmids, prophages, 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 (a term that is lately changing to in ...
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'' 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), 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.
Horizontal gene transfer is particularly active in bacterial genomes around the production of secondary or specialized metabolites.[Ginolhac, A., Jarrin, C., Robe, P., Perrière, G., Vogel, T. M., Simonet, P., & Nalin, R. (2005). Type I polyketide synthases may have evolved through horizontal gene transfer. Journal of Molecular Evolution, 60(6), 716-725.] This is clearly exhibited within certain groups of bacteria including ''P. aeruginosa'' and ''actinomycetales'', an order of ''Actinomycetota.'' Polyketide synthase
Polyketides are a class of natural products derived from a precursor molecule consisting of a chain of alternating ketone (or reduced forms of a ketone) and methylene groups: (-CO-CH2-). First studied in the early 20th century, discovery, biosynth ...
s (PKSs) and biosynthetic gene clusters provide modular organizations of associated genes making these bacteria well-adapted to acquire and discard helpful modular modifications via HGT. Certain areas of genes known as hotspots
Hotspot, Hot Spot or Hot spot may refer to:
Places
* Hot Spot, Kentucky, a community in the United States
Arts, entertainment, and media Fictional entities
* Hot Spot (comics), a name for the DC Comics character Isaiah Crockett
* Hot Spot (Tr ...
further increase the likelihood of horizontally transferred secondary metabolite-producing genes. The promiscuity of enzymes is a reoccurring theme in this particular theatre.
Bacterial transformation
Natural transformation
In category theory, a branch of mathematics, a natural transformation provides a way of transforming one functor into another while respecting the internal structure (i.e., the composition of morphisms) of the categories involved. Hence, a natur ...
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, catalase-positive bacterium, found in soil and the gastrointestinal tract of ruminants, humans and marine sponges. As a member of the genus ''Bacillus ...
'' 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 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 individuals of the appropriate s ...
, and is thus homologous to the resident chromosome. The capacity for natural transformation occurs in at least 67 prokaryotic species.[
Competence for transformation is typically induced by high cell density and/or nutritional limitation, conditions associated with the stationary phase of bacterial growth. Competence appears to be an adaptation for DNA repair. Transformation in bacteria can be viewed as a primitive sexual process, since it involves interaction of homologous DNA from two individuals to form recombinant DNA that is passed on to succeeding generations. Although transduction is the form of HGT most commonly associated with bacteriophages, certain phages may also be able to promote transformation.]
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 chang ...
in ''Mycobacterium smegmatis
''Mycobacterium smegmatis'' is an acid-fast bacterial species in the phylum ''Actinomycetota'' and the genus ''Mycobacterium''. It is 3.0 to 5.0 µm long with a bacillus shape and can be stained by Ziehl–Neelsen method and the auramine-rh ...
'', like conjugation in '' E. coli'', requires stable and extended contact between a donor and a recipient strain, is DNase resistant, and the transferred DNA is incorporated into the recipient chromosome by homologous recombination
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 cellular organisms but may ...
. However, unlike ''E. coli'' high frequency of recombination conjugation (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 ) is a domain of single-celled organisms. These microorganisms lack cell nuclei and are therefore prokaryotes. Archaea were initially classified as bacteria, receiving the name archaebacteria (in the Archaebact ...
''Sulfolobus solfataricus
''Saccharolobus solfataricus'' is a species of thermophilic archaeon. It was transferred from the genus ''Sulfolobus'' to the new genus ''Saccharolobus'' with the description of Saccharolobus caldissimus in 2018.
It was first isolated and disco ...
'', when UV irradiated, strongly induces the formation of type IV pili
A pilus (Latin for 'hair'; plural: ''pili'') is a hair-like appendage found on the surface of many bacteria and archaea. The terms ''pilus'' and '' fimbria'' (Latin for 'fringe'; plural: ''fimbriae'') can be used interchangeably, although some r ...
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 phylum Thermoproteota. ''S. acidocaldarius'' was the first ''Sulfolobus'' species to be described, in 1972 by Thomas D. Brock and collaborators. This species was ...
'', 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 cellular organisms but may ...
. 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, phylogenetics (; from Greek φυλή/ φῦλον [] "tribe, clan, race", and wikt:γενετικός, γενετικός [] "origin, source, birth") is the study of the evolutionary history and relationships among or within groups o ...
'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 sequences 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 mitochondria, cellular organelles within eukaryotic cells that convert chemical energy from food into a form that cells can use, such as adenosine triphosphate (ATP). Mitochondrial ...
s to the nuclear genome
Nuclear DNA (nDNA), or nuclear deoxyribonucleic acid, is the DNA contained within each cell nucleus of a eukaryotic organism. It encodes for the majority of the genome in eukaryotes, with mitochondrial DNA and plastid DNA coding for the rest. I ...
. As stated in the endosymbiotic theory, chloroplasts and mitochondria probably originated as bacterial endosymbiont
An ''endosymbiont'' or ''endobiont'' is any organism that lives within the body or cells of another organism most often, though not always, in a mutualistic relationship.
(The term endosymbiosis is from the Greek: ἔνδον ''endon'' "within ...
s of a progenitor to the eukaryotic cell.
Organelle to organelle
*Mitochondrial gene
Mitochondrial DNA (mtDNA or mDNA) is the DNA located in mitochondria, cellular organelles within eukaryotic cells that convert chemical energy from food into a form that cells can use, such as adenosine triphosphate (ATP). Mitochondrial D ...
s moved to parasites of the Rafflesiaceae
The Rafflesiaceae are a family of rare parasitic plants comprising 36 species in 3 genera found in the tropical forests of east and southeast Asia, including ''Rafflesia arnoldii'', which has the largest flowers of all plants. The plants are en ...
plant family from their hosts and from chloroplasts of a still-unidentified plant to the mitochondria of the bean '' Phaseolus''.
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 ( : fungi or funguses) is any member of the group of eukaryotic organisms that includes microorganisms such as yeasts and molds, as well as the more familiar mushrooms. These organisms are classified as a kingdom, separately from ...
, such as the yeast ''Saccharomyces cerevisiae
''Saccharomyces cerevisiae'' () (brewer's yeast or baker's yeast) is a species of yeast (single-celled fungus microorganisms). The species has been instrumental in winemaking, baking, and brewing since ancient times. It is believed to have b ...
''.
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 Oskar may refer to:
* oskar (gene), the Drosophila gene
* Oskar (given name) Oscar or Oskar is a masculine given name of Irish origin.
Etymology
The name is derived from two elements in Irish: the first, ''os'', means "deer"; the second element, ' ...
is an essential gene for the specification of the germline in Holometabola
Endopterygota (from Ancient Greek ''endon'' 'inner' + ''pterón'' 'wing' + New Latin ''-ota'' 'having'), also known as Holometabola, is a superorder of insects within the infraclass Neoptera that go through distinctive larval, pupal, and adult st ...
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. Tardigrade
Tardigrades (), known colloquially as water bears or moss piglets, are a phylum of eight-legged segmented micro-animals. They were first described by the German zoologist Johann August Ephraim Goeze in 1773, who called them Kleiner Wasserbä ...
s 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
''Caenorhabditis'' is a genus of nematodes which live in bacteria-rich environments like compost piles, decaying dead animals and rotting fruit. The name comes from Greek: caeno- (καινός (caenos) = new, recent); rhabditis = rod-like (ῥά ...
'' worms, and 12 ''Drosophila
''Drosophila'' () is a genus of flies, belonging to the family Drosophilidae, whose members are often called "small fruit flies" or (less frequently) pomace flies, vinegar flies, or wine flies, a reference to the characteristic of many speci ...
'' 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 adzuki bean beetle has acquired genetic material from its (non-beneficial) endosymbiont ''Wolbachia
''Wolbachia'' is a genus of intracellular bacteria that infects mainly arthropod species, including a high proportion of insects, and also some nematodes. It is one of the most common parasitic microbes, and is possibly the most common reproducti ...
''. New examples have recently been reported demonstrating that Wolbachia bacteria represent an important potential source of genetic material in arthropods and filarial nematodes.
*The psyllid ''Pachypsylla venusta'' has acquired genes from its current endosymbiont ''Carsonella'', and from many of its historical endosymbionts, too.
Plant to plant
*''Striga hermonthica
''Striga hermonthica'', commonly known as purple witchweed or giant witchweed, is a hemiparasitic plant that belongs to the family Orobanchaceae. It is devastating to major crops such as sorghum (''Sorghum bicolor'') and rice (''Oryza sativa'' ...
'', a parasitic
Parasitism is a close relationship between species, where one organism, the parasite, lives on or inside another organism, the host, causing it some harm, and is adapted structurally to this way of life. The entomologist E. O. Wilson ha ...
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
''Elysia chlorotica'' ( common name the eastern emerald elysia) is a small-to-medium-sized species of green sea slug, a marine opisthobranch gastropod mollusc. This sea slug superficially resembles a nudibranch, yet it does not belong to that ...
'' has been suggested by fluorescence in situ hybridization
Fluorescence ''in situ'' hybridization (FISH) is a molecular cytogenetic technique that uses fluorescent probes that bind to only particular parts of a nucleic acid sequence with a high degree of sequence complementarity. It was developed by ...
(FISH) analysis to contain photosynthesis-supporting genes obtained from an algae (''Vaucheria litorea
''Vaucheria litorea'' is a species of yellow-green algae (Xanthophyceae). It grows in a filamentous fashion (forming long tubular cells connected end to end). ''V. litorea'' is a common intertidal species of coastal brackish waters and salt mars ...
)'' 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
''Elysia chlorotica'' ( common name the eastern emerald elysia) is a small-to-medium-sized species of green sea slug, a marine opisthobranch gastropod mollusc. This sea slug superficially resembles a nudibranch, yet it does not belong to that ...
''.
*The whitefly ''Bemisia tabaci
The silverleaf whitefly (''Bemisia tabaci'', also informally referred to as the sweet potato whitefly) is one of several species of whitefly that are currently important agriculture, agricultural pest (animal), pests. A review in 2011 concluded t ...
'' acquired a plant detoxification gene that neutralizes plant toxins.
Plant to fungus
* Gene transfer between plants and fungi has been posited for a number of cases, including rice (''Oryza sativa
''Oryza sativa'', commonly known as Asian rice or indica rice, is the plant species most commonly referred to in English as ''rice''. It is the type of farmed rice whose cultivars are most common globally, and was first domesticated in the Yan ...
'').
* Evidence of gene transfer from plants was documented in the fungus ''Colletotrichum.''
* Plant expansin genes were transferred to fungi further enabling the fungi to infect plants.
Plant to bacteria
* Plant expansin genes were transferred to bacteria further enabling the bacteria to infect plants.
Fungi to insects
*Pea aphids (''Acyrthosiphon pisum
''Acyrthosiphon pisum'', commonly known as the pea aphid (and colloquially known as the green dolphin, pea louse, and clover louse), is a sap-sucking insect in the family Aphididae. It feeds on several species of legumes (plant family Fabaceae) ...
'') contain multiple genes from fungi
A fungus ( : fungi or funguses) is any member of the group of eukaryotic organisms that includes microorganisms such as yeasts and molds, as well as the more familiar mushrooms. These organisms are classified as a kingdom, separately from ...
. Plants, fungi, and microorganisms can synthesize carotenoids, but torulene made by pea aphid
Aphids are small sap-sucking insects and members of the superfamily Aphidoidea. Common names include greenfly and blackfly, although individuals within a species can vary widely in color. The group includes the fluffy white woolly aphids. A t ...
s is the only carotenoid known to be synthesized by an organism in the animal kingdom.
Fungi to fungi
* The toxin α-amanitin is found in numerous, seemingly unrelated genera fungi such as ''Amanita
The genus ''Amanita'' contains about 600 species of agarics, including some of the most toxic known mushrooms found worldwide, as well as some well-regarded edible species. This genus is responsible for approximately 95% of the fatalities resul ...
'', ''Lepiota
''Lepiota'' is a genus of gilled mushrooms in the family Agaricaceae. All ''Lepiota'' species are ground-dwelling saprotrophs with a preference for rich, calcareous soils. Basidiocarps (fruit bodies) are agaricoid with whitish spores, typically ...
'', and ''Galerina
''Galerina'' is a genus of small brown-spore saprobic fungi (colloquially often ''mushrooms''), with over 300 species found throughout the world from the far north to remote Macquarie Island in the Southern Ocean. The genus is most noted for some ...
''. Two biosynthetic genes involved in the production of α-amanitin are P450-29 and FMO1. Phylogenetic and genetic analyses of these genes strongly indicate that they were transferred between the genera via horizontal gene transfer.
Animals to animals
* Smelt
Smelt may refer to:
* Smelting, chemical process
* The common name of various fish:
** Smelt (fish), a family of small fish, Osmeridae
** Australian smelt in the family Retropinnidae and species ''Retropinna semoni''
** Big-scale sand smelt ''Ath ...
fish received antifreeze protein
Antifreeze proteins (AFPs) or ice structuring proteins refer to a class of polypeptides produced by certain animals, plants, fungi and bacteria that permit their survival in temperatures below the freezing point of water. AFPs bind to small ...
(AFP) gene from herring through a direct horizontal transfer.
Animals to bacteria
*The strikingly fish-like copper/zinc superoxide dismutase of '' Photobacterium leiognathi'' is most easily explained in terms of transfer of a gene from an ancestor of its fish host.
Human to protozoan
*The malaria
Malaria is a mosquito-borne infectious disease that affects humans and other animals. Malaria causes symptoms that typically include fever, tiredness, vomiting, and headaches. In severe cases, it can cause jaundice, seizures, coma, or death. S ...
pathogen
In biology, a pathogen ( el, πάθος, "suffering", "passion" and , "producer of") in the oldest and broadest sense, is any organism or agent that can produce disease. A pathogen may also be referred to as an infectious agent, or simply a germ ...
''Plasmodium vivax
''Plasmodium vivax'' is a protozoal parasite and a human pathogen. This parasite is the most frequent and widely distributed cause of recurring malaria. Although it is less virulent than ''Plasmodium falciparum'', the deadliest of the five huma ...
'' 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.
Compounds found to promote horizontal gene transfer
Through research into the growing issue of antibiotic resistance certain compounds have been observed to promote horizontal gene transfer. Antibiotics given to bacteria at non-lethal levels have been known to be a cause of antibiotic resistance but emerging research is now showing that certain non-antibiotic pharmaceuticals ( ibuprofen, naproxen
Naproxen is a nonsteroidal anti-inflammatory drug (NSAID) used to treat pain, menstrual cramps, inflammatory diseases such as rheumatoid arthritis, gout and fever. It is taken orally. It is available in immediate and delayed release formulat ...
, gemfibrozil, diclofenac
Diclofenac, sold under the brand name Voltaren, among others, is a nonsteroidal anti-inflammatory drug (NSAID) used to treat pain and inflammatory diseases such as gout. It is taken by mouth or rectally in a suppository, used by injection, or ...
, propranolol
Propranolol, sold under the brand name Inderal among others, is a medication of the beta blocker class. It is used to treat high blood pressure, a number of types of irregular heart rate, thyrotoxicosis, capillary hemangiomas, performance an ...
, etc.) also have a role in promoting antibiotic resistance through their ability to promote horizontal gene transfer (HGT) of genes responsible for antibiotic resistance. The transfer of antibiotic resistance genes (ARGs) through conjugation
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 chang ...
is significantly accelerated when donor cells with plasmids and recipient cells are introduced to each other in the presence of one of the pharmaceuticals. Non-antibiotic pharmaceuticals were also found to cause some responses in bacteria similar to those responses to antibiotics, such as increasing expression of the genes lexA, umuC, umuD and soxR involved in the bacteria's SOS response as well as other genes also expressed during exposure to antibiotics. These findings are from 2021 and due to the widespread use of non-antibiotic pharmaceuticals, more research needs to be done in order to further understanding on the issue.
Alongside non-antibiotic pharmaceuticals, other compounds relevant to antibiotic resistance have been tested such as malachite green
Malachite green is an organic compound that is used as a dyestuff and controversially as an antimicrobial in aquaculture. Malachite green is traditionally used as a dye for materials such as silk, leather, and paper. Despite its name the dye is ...
, ethylbenzene
Ethylbenzene is an organic compound with the formula . It is a highly flammable, colorless liquid with an odor similar to that of gasoline. This monocyclic aromatic hydrocarbon is important in the petrochemical industry as an reaction intermedia ...
, styrene
Styrene () is an organic compound with the chemical formula C6H5CH=CH2. This derivative of benzene is a colorless oily liquid, although aged samples can appear yellowish. The compound evaporates easily and has a sweet smell, although high concen ...
, 2,4-dichloroaniline Dichloroanilines are chemical compounds which consist of an aniline ring substituted with two chlorine atoms and have the molecular formula C6H5Cl2N. There are six isomers, varying in the positions of the chlorine atoms around the ring relative to ...
, trioxymethylene, o-xylene solutions, p-nitrophenol (PNP), p-aminophenol
4-Aminophenol (or ''para''-aminophenol or ''p''-aminophenol) is an organic compound with the formula H2NC6H4OH. Typically available as a white powder, it is commonly used as a developer for black-and-white film, marketed under the name Rodinal.
Re ...
(PAP), and phenol
Phenol (also called carbolic acid) is an aromatic organic compound with the molecular formula . It is a white crystalline solid that is volatile. The molecule consists of a phenyl group () bonded to a hydroxy group (). Mildly acidic, it ...
(PhOH). It is a global concern that ARGs have been found in wastewater treatment plants
Wastewater treatment is a process used to remove contaminants from wastewater and convert it into an effluent that can be returned to the water cycle. Once returned to the water cycle, the effluent creates an acceptable impact on the environmen ...
Textile
Textile is an umbrella term that includes various fiber-based materials, including fibers, yarns, filaments, threads, different fabric types, etc. At first, the word "textiles" only referred to woven fabrics. However, weaving is not the ...
wastewater has been found to contain 3- to 13-fold higher abundance of mobile genetic elements
Mobile genetic elements (MGEs) sometimes called selfish genetic elements are a type of genetic material that can move around within a genome, or that can be transferred from one species or replicon to another. MGEs are found in all organisms. In ...
than other samples of wastewater. The cause of this is the organic compounds used for textile dying (o-xylene, ethylbenzene, trioxymethylene, styrene, 2,4-dichloroaniline, and malachite green) raising the frequency of conjugative transfer when bacteria and plasmid (with donor) are introduced in the presence of these molecules. When textile wastewater combines with wastewater from domestic sewage, the ARGs present in wastewater are transferred at a higher rate due to the addition of textile dyeing compounds increasing the occurrence of HGT.
Other organic pollutants commonly found in wastewater have been the subject of similar experiments. A 2021 study used similar methods of using plasmid in a donor and mixing that with a receptor in the presence of compound in order to test horizontal gene transfer of antibiotic resistance genes but this time in the presence of phenolic compounds. Phenolic compounds are commonly found in wastewater and have been found to change functions and structures of the microbial communities Microbial population biology is the application of the principles of population biology to microorganisms.
Distinguishing from other biological disciplines
Microbial population biology, in practice, is the application of population ecology and popu ...
during the wastewater treatment process. Additionally, HGT increases in frequency in the presence of the compounds p-nitrophenol (PNP), p-aminophenol (PAP), and phenol. These compounds result in a 2- to 9-fold increase in HGT (p-nitrophenol being on the lower side of 2-fold increases and p-aminophenol and phenol having a maximum increase of 9-fold). This increase in HGT is on average less than the compounds ibuprofen, naproxen, gemfibrozil, diclofenac, propranolol, o-xylene, ethylbenzene, trioxymethylene, styrene, 2,4-dichloroaniline, and malachite green but their increases is still significant. The study that came to this conclusion is similar to the study on horizontal gene transfer and non-antibiotic pharmaceuticals in that it was done in 2021 and leaves room for more research, specifically in the focus of the study which is activated sludge
The activated sludge process is a type of biological wastewater treatment process for treating sewage or industrial wastewaters using aeration and a biological floc composed of bacteria and protozoa. It uses air (or oxygen) and microorganism ...
.
Heavy metals have also been found to promote conjugative transfer of antibiotic resistance genes. The paper that led to the discovery of this was done in 2017 during the emerging field of horizontal gene transfer assisting compound research. Metals assist in the spread of antibiotic resistance through both co-resistance as well as cross-resistance
Cross-resistance is when something develops resistance to several substances that have a similar mechanism of action. For example, if a certain type of bacteria develops resistance to one antibiotic, that bacteria will also have resistance to sev ...
mechanisms. In quantities relevant to the environment, Cu(II), Ag(I), Cr(VI)
Hexavalent chromium (chromium(VI), Cr(VI), chromium 6) is chromium in any chemical compound that contains the element in the +6 oxidation state (thus hexavalent). Virtually all chromium ore is processed via hexavalent chromium, specifically the ...
, and Zn(II) promote HGT from donor and receptor strains of E. coli. The presence of these metals triggered SOS response from bacterial cells and made the cells more permeable. These are the mechanisms that make even low levels of heavy metal pollution in the environment impact HGT and therefore the spread of ARGs.
Artificial horizontal gene transfer
Genetic engineering is essentially horizontal gene transfer, albeit with synthetic expression cassettes. The Sleeping Beauty transposon system
The ''Sleeping Beauty'' transposon system is a synthetic DNA transposon designed to introduce precisely defined DNA sequences into the chromosomes of vertebrate animals for the purposes of introducing new traits and to discover new genes and the ...
(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 confounding factor
In statistics, a confounder (also confounding variable, confounding factor, extraneous determinant or lurking variable) is a variable that influences both the dependent variable and independent variable, causing a spurious association. Con ...
in inferring phylogenetic trees based on the sequence
In mathematics, a sequence is an enumerated collection of objects in which repetitions are allowed and order matters. Like a set, it contains members (also called ''elements'', or ''terms''). The number of elements (possibly infinite) is calle ...
of one gene.[Graham Lawton ]
Why Darwin was wrong about the tree of life
' New Scientist
''New Scientist'' is a magazine covering all aspects of science and technology. Based in London, it publishes weekly English-language editions in the United Kingdom, the United States and Australia. An editorially separate organisation publish ...
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 that lacks a nucleus and other membrane-bound organelles. The word ''prokaryote'' comes from the Greek πρό (, 'before') and κάρυον (, 'nut' or 'kernel').Campbell, N. "Biology:Concepts & Conne ...
s is the 16S ribosomal RNA
16 S ribosomal RNA (or 16 S rRNA) is the RNA component of the 30S subunit of a prokaryotic ribosome ( SSU rRNA). It binds to the Shine-Dalgarno sequence and provides most of the SSU structure.
The genes coding for it are referred to as 16S rR ...
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 network
A phylogenetic network is any graph used to visualize evolutionary relationships (either abstractly or explicitly) between nucleotide sequences, genes, chromosomes, genomes, or species. They are employed when reticulation events such as hybrid ...
s.
Using single genes as phylogenetic markers, it is difficult to trace organismal phylogeny
A phylogenetic tree (also phylogeny or evolutionary tree Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, MA.) is a branching diagram or a tree showing the evolutionary relationships among various biological spe ...
in the presence of horizontal gene transfer. Combining the simple coalescence
Coalescence may refer to:
* Coalescence (chemistry), the process by which two or more separate masses of miscible substances seem to "pull" each other together should they make the slightest contact
* Coalescence (computer science), the merging of ...
model of cladogenesis
Cladogenesis is an evolutionary splitting of a parent species into two distinct species, forming a clade.
This event usually occurs when a few organisms end up in new, often distant areas or when environmental changes cause several extinctions, ...
with rare HGT horizontal gene transfer events suggest there was no single most recent common ancestor
In biology and genetic genealogy, the most recent common ancestor (MRCA), also known as the last common ancestor (LCA) or concestor, of a set of organisms is the most recent individual from which all the organisms of the set are descended. The ...
that contained all of the genes ancestral to those shared among the three domains of life
Life is a quality that distinguishes matter that has biological processes, such as Cell signaling, signaling and self-sustaining processes, from that which does not, and is defined by the capacity for Cell growth, growth, reaction to Stimu ...
. Each contemporary molecule
A molecule is a group of two or more atoms held together by attractive forces known as chemical bonds; depending on context, the term may or may not include ions which satisfy this criterion. In quantum physics, organic chemistry, and bioche ...
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
The last universal common ancestor (LUCA) is the most recent population from which all organisms now living on Earth share common descent—the most recent common ancestor of all current life on Earth. This includes all cellular organisms; th ...
(LUCA) at the root of the tree of life
The tree of life is a fundamental archetype in many of the world's mythological, religious, and philosophical traditions. It is closely related to the concept of the sacred tree.Giovino, Mariana (2007). ''The Assyrian Sacred Tree: A Hist ...
first formulated by Carl Woese
Carl Richard Woese (; July 15, 1928 – December 30, 2012) was an American microbiologist and biophysicist. Woese is famous for defining the Archaea (a new domain of life) in 1977 through a pioneering phylogenetic taxonomy of 16S ribosomal RNA, ...
, 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 fulgidus
''Archaeoglobus'' is a genus of the phylum Euryarchaeota. ''Archaeoglobus'' can be found in high-temperature oil fields where they may contribute to oil field souring.
Metabolism
''Archaeoglobus'' grow anaerobically at extremely high temperat ...
'' was seen as an anomaly with respect to a phylogenetic tree based upon the encoding for the enzyme
Enzymes () are proteins that act as biological catalysts by accelerating chemical reactions. The molecules upon which enzymes may act are called substrates, and the enzyme converts the substrates into different molecules known as products ...
HMGCoA reductase
HMG-CoA reductase (3-hydroxy-3-methyl-glutaryl-coenzyme A reductase, official symbol HMGCR) is the rate-controlling enzyme (NADH-dependent, ; NADPH-dependent, ) of the mevalonate pathway, the metabolic pathway that produces cholesterol and oth ...
—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
Symbiogenesis (endosymbiotic theory, or serial endosymbiotic theory,) is the leading evolutionary theory of the origin of eukaryotic cells from prokaryotic organisms. The theory holds that mitochondria, plastids such as chloroplasts, and pos ...
, that mitochondria in eukaryotes derived from alpha-proteobacterial cells and that chloroplasts came from ingested cyanobacteria, and other gene transfers may have affected early eukaryotes. (In contrast, multicellular eukaryotes have mechanisms to prevent horizontal gene transfer, including separated germ cell
Germ or germs may refer to:
Science
* Germ (microorganism), an informal word for a pathogen
* Germ cell, cell that gives rise to the gametes of an organism that reproduces sexually
* Germ layer, a primary layer of cells that forms during emb ...
s.) 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
Lycopene is an organic compound classified as a tetraterpene and a carotene. Lycopene (from the neo-Latin '' Lycopersicum'', the tomato species) is a bright red carotenoid hydrocarbon found in tomatoes and other red fruits and vegetables.
Occu ...
cyclase A cyclase is an enzyme, almost always a lyase, that catalyzes a chemical reaction to form a cyclic compound. Important cyclase enzymes include:
* Adenylyl cyclase, which forms cyclic AMP from adenosine triphosphate (EC 4.6.1.1)
** ADCY1
** ADCY2 ...
for carotenoid biosynthesis, between Chlorobiota
The green sulfur bacteria are a phylum of obligately anaerobic photoautotrophic bacteria that metabolize sulfur.
Green sulfur bacteria are nonmotile (except ''Chloroherpeton thalassium'', which may glide) and capable of anoxygenic photosynthes ...
and " Cyanobacteria".
*''TetO'' gene conferring resistance to tetracycline
Tetracycline, sold under various brand names, is an oral antibiotic in the tetracyclines family of medications, used to treat a number of infections, including acne, cholera, brucellosis, plague, malaria, and syphilis.
Common side effects in ...
, between ''Campylobacter jejuni
''Campylobacter jejuni'' () is a species of pathogenic bacteria, one of the most common causes of food poisoning in Europe and in the US. The vast majority of cases occur as isolated events, not as part of recognized outbreaks. Active surveillan ...
''.
*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 phytophagous
A herbivore is an animal anatomically and physiologically adapted to eating plant material, for example foliage or marine algae, for the main component of its diet. As a result of their plant diet, herbivorous animals typically have mouthpar ...
mite
Mites are small arachnids (eight-legged arthropods). Mites span two large orders of arachnids, the Acariformes and the Parasitiformes, which were historically grouped together in the subclass Acari, but genetic analysis does not show clear e ...
s and Lepidoptera allowing the detoxification of cyanogenic glucosides produced by host plants.
*The LINE1 sequence has transferred from humans to the gonorrhea
Gonorrhea, colloquially known as the clap, is a sexually transmitted infection (STI) caused by the bacterium ''Neisseria gonorrhoeae''. Infection may involve the genitals, mouth, or rectum. Infected men may experience pain or burning with u ...
bacteria.
See also
*Agrobacterium
''Agrobacterium'' is a genus of Gram-negative bacteria established by H. J. Conn that uses horizontal gene transfer to cause tumors in plants. '' Agrobacterium tumefaciens'' is the most commonly studied species in this genus. ''Agrobacterium'' i ...
, a bacterium well known for its ability to transfer DNA between itself and plants.
* Endogenous retrovirus
* Genetically modified organism
* Inferring horizontal gene transfer
*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 (a term that is lately changing to in ...
*Mobile genetic elements
Mobile genetic elements (MGEs) sometimes called selfish genetic elements are a type of genetic material that can move around within a genome, or that can be transferred from one species or replicon to another. MGEs are found in all organisms. In ...
*Phylogenetic network
A phylogenetic network is any graph used to visualize evolutionary relationships (either abstractly or explicitly) between nucleotide sequences, genes, chromosomes, genomes, or species. They are employed when reticulation events such as hybrid ...
* Phylogenetic tree
* Provirus
*Reassortment
Reassortment is the mixing of the genetic material of a species into new combinations in different individuals. Several different processes contribute to reassortment, including assortment of chromosomes, and chromosomal crossover. It is particul ...
*Retrotransposon
Retrotransposons (also called Class I transposable elements or transposons via RNA intermediates) are a type of genetic component that copy and paste themselves into different genomic locations (transposon) by converting RNA back into DNA through ...
*Symbiogenesis
Symbiogenesis (endosymbiotic theory, or serial endosymbiotic theory,) is the leading evolutionary theory of the origin of eukaryotic cells from prokaryotic organisms. The theory holds that mitochondria, plastids such as chloroplasts, and pos ...
*Tree of life (biology)
The tree of life or universal tree of life is a metaphor, model and research tool used to explore the evolution of life and describe the relationships between organisms, both living and extinct, as described in a famous passage in Charles Dar ...
*Xenobiology
Xenobiology (XB) is a subfield of synthetic biology, the study of synthesizing and manipulating biological devices and systems. The name "xenobiology" derives from the Greek word ''xenos'', which means "stranger, alien". Xenobiology is a form o ...
References
Further reading
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– Papers by Dr Michael Syvanen on Horizontal Gene Transfer
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* This article seeks to shift the emphasis in early phylogenic adaptation from vertical to horizontal gene transfer. He uses the term "Darwinian Threshold" for the time of major transition of evolutionary mechanisms from mostly horizontal to mostly vertical transfer, and the "origin of speciation".
* 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.
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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
Microbial population biology
Modification of genetic information