So according to a PPT I'm reading, bacterial conjugation works by the two bacteria joining pili and exchanging plasmids. So how exactly do the plasmids get across the gap? If I understand this correctly, the pili are little hair-like things on the outside of the bacteria -- so unless the plasmids were actually able to somehow be pushed through the pili, there would be gap. Right?
The only other possibility I can think of would be that the membranes fused or something like that. But that comes with it's own whole set of problems.
How does this work?
The donor cell retracts it pilus upon contact with another cell and both cells form a pore between the two cells, which allows the transfer of DNA. Take a look at the image, I think this makes it clearer (from the Wikipedia article on Pili):
This has even be seen in an electron microscope:
Horizontal Gene Transfer
Horizontal, or lateral, gene transfer is generally defined as exchange of genetic information between contemporary organisms. Horizontal transfer is distinct from vertical transfer by which genetic information is passed from parent to offspring. A special case of the horizontal transfer involves the transfer of DNA between chloroplast or mitochondrial and nuclear genomes. In addition to entire genes, parts of genes, such as exons or introns, may also be transferred in this way. Although horizontal transfer is more likely to be successful between closely related than distantly related species, it does occur between species as divergent as those found in different domains of life.
3 Modes of Genetic Transfer in Bacterial Cells |Biology
Three modes of genetic transfer in bacterial Cells are : (a) Transformation, (b) Transduction, (c) Conjugation.
Bacteria divide very rapidly. The doubling time is also called generation time and it may be as low as 20 minutes. Bacteria mainly reproduce by asexual reproduction but do not exhibit true sexual reproduction as they do not produce diploid phase. Thus, meiosis is lacking. However, bacteria exchange genetic material between two cells.
Modes of genetic transfer in bacteria:
Three modes of genetic transfer between bacterial cells are:
The phenomenon by which DNA isolated from one type of cell, when introduced into another type is able to bestow some of its properties into the latter, is referred to as transformation. It was confirmed by Griffith with his experiments on bacteria Streptococcus pneumonia.
The transfer of genetic material from one bacterium to another through bacteriophage is called transduction.
The unidirectional transfer of DNA from one cell to another through a cytoplasmic bridge is called conjugation. The process is equivalent to sexual mating in eukaryotes. Two bacterial haploid cells of different strains come close to each other.
They recognise each other by complementary macromolecules borne on their surface. Donor or male cell passes part or whole of the chromosome into recipient or female cell. The ability of transferring the genetic material from male is controlled by sex or fertility factor (F gene) present in a plasmid.
Thus, genes can be transferred from donor to recipient cell on a molecule of DNA which acts as sex factor called F gene. This sex gene can reside in a bacterial chromosome or it may exist as an autonomous unit in cytoplasm.
Male bacterium with thorn-like protuberances called as sex pili come in contact with female bacterium which lacks pili and donate its DNA. F factor (a plasmid) carries genes for producing pili and other functions required to transfer DNA. At times F factor integrates into bacterial chromosome.
Such bacteria can transfer their genetic material into female cell with high frequency (Hfr) in a particular sequence. They are called as Hfr -strains. Conjugation was first demonstrated by Lederberg and Tatum in E. coli. The frequency of recombination was very low in Lederberg’s experiments.
The Hfr cell acts as the male bacterium and when mixed with the female (F—) cell forms a conjugation bridge. The F factor containing DNA breaks at a particular point and starts inserting the DNA into the female and the sequence of chromosomal gene transfer is always in the same order (A, B, C and D genes).
The F factor is transferred last. The conjugation bridge usually breaks before the entire chromosome is transferred. Only the genes A and B have been transferred in the example given. These A and/or B genes can recombine with the corresponding genes in the F— chromosome.
Thus, if B’ in the F— cell is a mutated form of B, theft the B’ in the F— chromosome can become B as a result of recombination after conjugation. Thus, genetic markers can be transferred from a host to a suitable recipient lacking such markers.
The order in which such markers are transferred to the recipient would follow the order in which they are present in the donor. Thus, conjugation experiments are useful in constructing the gene maps (order of arrangement of genes in the chromosome) of organisms.
Hayes (1952) found a strain of E. coli in which the frequency of recombination was as high as 100 to 1000 times as reported by Lederberg. The strain was called high frequency recombinant (Hfr) strain.
Mobile bacterial genetic elements
Mobile genetic elements fall into two general types elements that can move from one bacterial cell to another, which in terms of antibiotic resistance includes resistance plasmids and conjugative resistance transposons, and elements that can move from one genetic location to another in the same cell. The latter elements include resistance transposons, gene cassettes and ISCR-promoted gene mobilization. Plasmids and conjugative transposons transfer from one cell to another by mechanisms that involve replication. Transposons, gene cassettes and ISCR-mediated gene transfer between sites on the same or on different DNA molecules require some form of recombination, which may or may not also include some form of replication (Bennett, 2005). Plasmids accumulate antibiotic resistance genes as a consequence of the activities of at least these three recombination systems.
How does gene transfer occur in bacteria?
Horizontal gene transfer may occur via three main mechanisms: transformation, transduction or conjugation. Transformation involves uptake of short fragments of naked DNA by naturally transformable bacteria. Transduction involves transfer of DNA from one bacterium into another via bacteriophages.
Likewise, how is chromosomal DNA transferred between bacteria? Conjugation. In conjugation, DNA is transferred from one bacterium to another. After the donor cell pulls itself close to the recipient using a structure called a pilus, DNA is transferred between cells. An F+ donor cell contains its chromosomal DNA and an F plasmid.
Keeping this in consideration, how does gene transfer work?
In transduction, DNA is transmitted from one cell to another via a bacteriophage. In horizontal gene transfer, newly acquired DNA is incorporated into the genome of the recipient through either recombination or insertion. Insertion occurs when the foreign DNA introduced into a cell shares no homology with existing DNA.
What is meant by gene transfer?
Gene transfer: The insertion of unrelated genetic information in the form of DNA into cells. There are also different ways to transfer genes. Some of these methods involve the use of a vector such as a virus that has been specifically modified so it can take the gene along with it when it enters the cell.
Unlike the last three methods which can be used in prokaryotes, transfection is only done in eukaryotic cells. Transfection is the process by which foreign DNA is deliberately introduced into a eukaryotic cell through non-viral methods including both chemical and physical methods in the lab. Chemicals like calcium phosphate and diethylaminoehtyl (DEAE)-dextra neutralize or even impart an overall positive charge on DNA molecules so that it can more easily cross the negatively charged cell membrane. Physical methods such as electroporation or microinjection actually pokes holes in the cell membrane so DNA can be introduced directly into the cell. Microinjection requires the use of a fine needle to deliver nucleic acids to individual cells. Electroporation on the other hand uses electrical pulses to create transient pores in the cell membrane that genetic material can pass through.
If you are starting any molecular biology experiment check out Addgene’s protocol page, which has both protocols and videos for techniques in basic molecular biology, plasmid cloning, and viruses.
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Horizontal Gene Transfer
Horizontal DNA transfer is the exchange of genes between two cells of the same generation, as opposed to from parent to progeny.
Normally, genes and the characteristics they code for are passed down from parent to progeny. This is called vertical gene transfer and is why you have half of the charecteristics of your mother, and half of your father. Bacteria and some lower eukaryotes are unique in that they can pass DNA from one cell of the same generation to another. We refer to this as Horizontal Gene Transfer (see diagram below).
There are three ways for bacteria to transfer their DNA horizontally:
Conjugation is the transfer of DNA directly from one cell to another through cell-cell contact. The DNA transferred by conjugation often involve plasmids. Plasmids are circular pieces of DNA that can replicate in the bacterial cell, independently of the chromosome. The conjugative transfer of plasmids is carried out by cell surface structures that act like syringes, injecting the plasmid into neighbouring cells.
You can watch a video describing conjugation by clicking here.
Unlike humans, bacteria are capable of taking up DNA directly from their enviroment and incorporating it into their genomes.This process is known as natural transformation. This DNA usually comes from dead bacteria lysing (splitting open) and releasing their genetic contents into the surrounding area.
Transduction is the transfer of DNA from one cell to another by a virus. These viruses are known as bacteriophage and they specifically infect bacteria. Bacteriophage don't have the machinery to replicate their own genomes or express their own genes, so instead, they hijjack the bacterial machinery to do so. Host cells will continue to express phage proteins and replicate the phage genome forming new virus particles. This process continues until the cell is so full of phage particles that it splits open (lyses), releasing phage into the surrounding area. This is known as the lytic cycle. Some phage can switch between this life cycle and a state of lysogeny, where they combine their genome with the bacterial chromosome, and remain silent for many generations. When lysogenic phage remove (excise) their genomes from the host chromosome, they occasionally take small sequences of bacterial DNA with them. Phage genome containing bacterial DNA is then packaged into phage coat proteins to form a complete, recombinant virus particle. When these phage lyse the bacterial cell and re-infect a new host, they take bacterial DNA with them.
Click here to watch a narrated animation about phage transduction.
Conjugation is the transfer of circular DNA called plasmids through cell to cell contact. Transformation is the uptake of 'free' DNA from the environment. Transduction is the transfer of DNA by bacteria-specific viruses called bacteriophage.
Horizontal transfer of antibiotic resistance genes in clinical environments
A global medical crisis is unfolding as antibiotics lose effectiveness against a growing number of bacterial pathogens. Horizontal gene transfer (HGT) contributes significantly to the rapid spread of resistance, yet the transmission dynamics of genes that confer antibiotic resistance are poorly understood. Multiple mechanisms of HGT liberate genes from normal vertical inheritance. Conjugation by plasmids, transduction by bacteriophages, and natural transformation by extracellular DNA each allow genetic material to jump between strains and species. Thus, HGT adds an important dimension to infectious disease whereby an antibiotic resistance gene (ARG) can be the agent of an outbreak by transferring resistance to multiple unrelated pathogens. Here, we review the small number of cases where HGT has been detected in clinical environments. We discuss differences and synergies between the spread of plasmid-borne and chromosomal ARGs, with a special consideration of the difficulties of detecting transduction and transformation by routine genetic diagnostics. We highlight how 11 of the top 12 priority antibiotic-resistant pathogens are known or predicted to be naturally transformable, raising the possibility that this mechanism of HGT makes significant contributions to the spread of ARGs. HGT drives the evolution of untreatable "superbugs" by concentrating ARGs together in the same cell, thus HGT must be included in strategies to prevent the emergence of resistant organisms in hospitals and other clinical settings.
Keywords: antibiotic resistance conjugaison conjugation horizontal gene transfer natural transformation résistance aux antibiotiques transduction transfert horizontal de gènes transformation naturelle.
We are grateful to Enago (www.enago.jp) for English editing and proofreading services.
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Keywords : plasmid transformation, horizontal plasmid transfer, Escherichia coli, antibiotic resistance, solid-air biofilm
Citation: Hasegawa H, Suzuki E and Maeda S (2018) Horizontal Plasmid Transfer by Transformation in Escherichia coli: Environmental Factors and Possible Mechanisms. Front. Microbiol. 9:2365. doi: 10.3389/fmicb.2018.02365
Received: 21 June 2018 Accepted: 14 September 2018
Published: 04 October 2018.
Dongchang Sun, Zhejiang University of Technology, China
Nathalie J. A. Campo, UMR5100 Laboratoire de Microbiologie et Génétique Molຜulaires (LMGM), France
Rosemary Redfield, The University of British Columbia, Canada
Radoslaw Pluta, Institute for Research in Biomedicine, Spain
Copyright © 2018 Hasegawa, Suzuki and Maeda. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
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 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 (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.  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.   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 prokaryotes"  (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 evolution." 
Grafting of one plant to another can transfer chloroplasts (organelles in plant cells that conduct photosynthesis), mitochondrial DNA, and the entire cell nucleus containing the genome to potentially make a new species.  Some Lepidoptera (e.g. monarch butterflies and silkworms) have been genetically modified by horizontal gene transfer from the wasp bracovirus.  Bites from insects in the family Reduviidae (assassin bugs) can, via a parasite, infect humans with the trypanosomal 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 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". 
There are several mechanisms for horizontal gene transfer:   
- , the genetic alteration of a cell resulting from the introduction, uptake and expression of foreign genetic material (DNA or RNA).  This process is relatively common in bacteria, but less 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 and biotechnology. , the process in which bacterial DNA is moved from one bacterium to another by a virus (a bacteriophage, or phage).  , 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.  , virus-like elements encoded by the host that are found in the alphaproteobacteria order Rhodobacterales. 
Horizontal transposon transfer Edit
A transposable element (TE) (also called a transposon or jumping gene) is a mobile segment of DNA that can sometimes pick up a resistance gene and insert it into a plasmid or chromosome, thereby inducing horizontal gene transfer of antibiotic resistance. 
Horizontal transposon transfer (HTT) refers to the passage of pieces of DNA that are characterized by their ability to move from one locus to another between genomes by means other than parent-to-offspring inheritance. Horizontal gene transfer has long been thought to be crucial to prokaryotic evolution, but there is a growing amount of data showing that HTT is a common and widespread phenomenon in eukaryote evolution as well.  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 transposons and LTR retroelements are more likely to be capable of HTT because both have a stable, double-stranded DNA intermediate that is thought to be sturdier than the single-stranded RNA intermediate of non-LTR retroelements, which can be highly degradable.  Non-autonomous elements may be less likely to transfer horizontally compared to autonomous elements because they do not encode the proteins required for their own mobilization. The structure of these non-autonomous elements generally consists of an intronless gene encoding a transposase protein, and may or may not have a promoter sequence. Those that do not have promoter sequences encoded within the mobile region rely on adjacent host promoters for expression.  Horizontal transfer is thought to play an important role in the TE life cycle. 
HTT has been shown to occur between species and across continents in both 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 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. 
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.
The virus called Mimivirus infects amoebae. Another virus, called Sputnik, also infects amoebae, but it cannot reproduce unless mimivirus has already infected the same cell.  "Sputnik's genome reveals further insight into its biology. Although 13 of its genes show little similarity to any other known genes, three are closely related to mimivirus and mamavirus genes, perhaps cannibalized by the tiny virus as it packaged up particles sometime in its history. This suggests that the satellite virus could perform horizontal gene transfer between viruses, paralleling the way that bacteriophages ferry genes between bacteria."  Horizontal transfer is also seen between geminiviruses and tobacco plants. 
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   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 exoenzymes, amongst bacteria.  A prime example concerning the spread of exotoxins is the adaptive evolution of Shiga toxins in E. coli through horizontal gene transfer via transduction with Shigella species of bacteria.  Strategies to combat certain bacterial infections by targeting these specific virulence factors and mobile genetic elements have been proposed.  For example, horizontally transferred genetic elements play important roles in the virulence of E. coli, Salmonella, Streptococcus and Clostridium perfringens. 
In prokaryotes, restriction-modification systems are known to provide immunity against horizontal gene transfer and in stabilizing mobile genetic elements. Genes encoding restriction modification systems have been reported to move between prokaryotic genomes within mobile genetic elements (MGE) such as plasmids, prophages, insertion sequences/transposons, integrative conjugative elements (ICE),  and integrons. 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.
Bacterial transformation Edit
Natural transformation is a bacterial adaptation for DNA transfer (HGT) that depends on the expression of numerous bacterial genes whose products are responsible for this process.   In general, transformation is a complex, energy-requiring developmental process. In order for a bacterium to bind, take up and recombine exogenous DNA into its chromosome, it must become competent, that is, enter a special physiological state. Competence development in Bacillus subtilis requires expression of about 40 genes.  The DNA integrated into the host chromosome is usually (but with infrequent exceptions) derived from another bacterium of the same species, and is thus homologous to the resident chromosome. The capacity for natural transformation occurs in at least 67 prokaryotic species.  Competence for transformation is typically induced by high cell density and/or nutritional limitation, conditions associated with the stationary phase of bacterial growth. Competence appears to be an adaptation for DNA repair.  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 Edit
Conjugation in Mycobacterium smegmatis, like conjugation in E. coli, requires stable and extended contact between a donor and a recipient strain, is DNase resistant, and the transferred DNA is incorporated into the recipient chromosome by homologous recombination. However, unlike E. coli high frequency of recombination conjugation (Hfr), mycobacterial conjugation is a type of HGT that is chromosome rather than plasmid based.  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 Edit
The archaeon Sulfolobus solfataricus, when UV irradiated, strongly induces the formation of type IV pili 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, 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.  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.
"Sequence comparisons suggest recent horizontal transfer of many genes among diverse species including across the boundaries of phylogenetic 'domains'. Thus determining the phylogenetic history of a species can not be done conclusively by determining evolutionary trees for single genes." 
Organelle to nuclear genome Edit
- Analysis of DNA sequences suggests that horizontal gene transfer has occurred within eukaryotes from the chloroplast and mitochondrial genomes to the nuclear genome. As stated in the endosymbiotic theory, chloroplasts and mitochondria probably originated as bacterial endosymbionts of a progenitor to the eukaryotic cell. 
Organelle to organelle Edit
- moved to parasites of the Rafflesiaceae plant family from their hosts  and from chloroplasts of a still-unidentified plant to the mitochondria of the bean Phaseolus. 
Viruses to plants Edit
Bacteria to fungi Edit
Bacteria to plants Edit
- 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 Edit
- is a gene in the genome of the coffee borer beetle (Hypothenemus hampei) that resembles bacterial genes, and is thought to be transferred from bacteria in the beetle's gut. 
Bacteria to animals Edit
Endosymbiont to insects and nematodes Edit
- The 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 filarialnematodes. 
Plant to plant Edit
- Striga hermonthica, a parasiticeudicot, 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 Edit
- 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 Edit
Fungi to insects Edit
- Pea aphids (Acyrthosiphon pisum) contain multiple genes from 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 Edit
Human to protozoan Edit
- The malariapathogenPlasmodium vivax acquired genetic material from humans that might help facilitate its long stay in the body. 
Human genome Edit
- 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. 
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.   (See also Gene therapy.)
Horizontal gene transfer is a potential confounding factor in inferring phylogenetic trees based on the sequence of one gene.  For example, given two distantly related bacteria that have exchanged a gene a phylogenetic tree including those species will show them to be closely related because that gene is the same even though most other genes are dissimilar. For this reason, it is often ideal to use other information to infer robust phylogenies such as the presence or absence of genes or, more commonly, to include as wide a range of genes for phylogenetic analysis as possible.
For example, the most common gene to be used for constructing phylogenetic relationships in prokaryotes is the 16S ribosomal RNA gene since its sequences tend to be conserved among members with close phylogenetic distances, but variable enough that differences can be measured. However, in recent years it has also been argued that 16s rRNA genes can also be horizontally transferred. Although this may be infrequent, the validity of 16s rRNA-constructed phylogenetic trees must be reevaluated. 
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 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 Edit
Horizontal gene transfer poses a possible challenge to the concept of the last universal common ancestor (LUCA) at the root of the tree of life first formulated by Carl Woese, which led him to propose the Archaea as a third domain of life.  Indeed, it was while examining the new three-domain view of life that horizontal gene transfer arose as a complicating issue: Archaeoglobus fulgidus was seen as an anomaly with respect to a phylogenetic tree based upon the encoding for the enzyme HMGCoA reductase—the organism in question is a definite Archaean, with all the cell lipids and transcription machinery that are expected of an Archaean, but whose HMGCoA genes are of bacterial origin.  Scientists are broadly agreed on symbiogenesis, that mitochondria in eukaryotes derived from alpha-proteobacterial cells and that chloroplasts came from ingested cyanobacteria, and other gene transfers may have affected early eukaryotes. (In contrast, multicellular eukaryotes have mechanisms to prevent horizontal gene transfer, including separated germ cells.) If there had been continued and extensive gene transfer, there would be a complex network with many ancestors, instead of a tree of life with sharply delineated lineages leading back to a LUCA.   However, a LUCA can be identified, so horizontal transfers must have been relatively limited. 
Phylogenetic information in HGT Edit
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 Edit
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. 
There is evidence for historical horizontal transfer of the following genes: