Horizontal gene transfer
Horizontal gene transfer or lateral gene transfer is the movement of genetic material between organisms other than by the transmission of DNA from parent to offspring. 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 that can degrade novel compounds such as human-created pesticides and in the evolution, maintenance, and transmission of virulence. It often involves temperate 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, transduction and conjugation, 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. HGT events are thought to occur less frequently in eukaryotes than in prokaryotes. However, growing evidence indicates that HGT is relatively common among many eukaryotic species and can have an impact on adaptation to novel environments. Its study, however, is hindered by the complexity of eukaryotic genomes and the abundance of repeat-rich regions, which complicate the accurate identification and characterization of transferred genes.
It is postulated that HGT promotes the maintenance of a universal life biochemistry and, subsequently, the universality of the genetic code.
History
, 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 1940s 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, simultaneously revealing the mechanism of diphtheria, 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 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 put it: "Increasingly, studies of genes and genomes are indicating that considerable horizontal transfer has occurred between prokaryotes". The phenomenon appears to have had some significance for unicellular eukaryotes as well. As Bapteste et al. 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, mitochondrial DNA, and the entire cell nucleus containing the genome to potentially make a new species. Some Lepidoptera have been genetically modified by horizontal gene transfer from the wasp bracovirus. Bites from insects in the family Reduviidae 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 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 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, the genetic alteration of a cell resulting from the introduction, uptake and expression of foreign genetic material. 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.
- Transduction, the process in which bacterial DNA is moved from one bacterium to another by a virus.
- 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 agents, virus-like elements encoded by the host that are found in the alphaproteobacteria order Rhodobacterales.
Horizontal transposon transfer
Horizontal transposon transfer 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. In plants, it appears that LTR retrotransposons of the Copia superfamilies, especially those with low copy numbers from the Ale and Ivana lineages, are more likely to undergo horizontal transfer between different plant species.
HTT has been shown to occur between species and across continents in both plants and animals, 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. In plants, the interaction between lianas and trees has been shown to facilitate HTT in natural ecosystems. Successful transfer of a transposable element requires delivery of DNA from donor to host cell, 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, 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.
Methods of detection
Horizontal gene transfer is typically inferred using bioinformatics methods, either by identifying atypical sequence signatures or by identifying strong discrepancies between the evolutionary history of particular sequences compared to that of their hosts. The transferred gene found in the receiving species is more closely related to the genes of the donor species than would be expected.One demonstrated method to find HGT events is through Shotgun Metagenomics; breaking down then sequencing DNA in a sample by its contiguous regions and looking for phylogenetic mismatches, which can be inferred as instances of Horizontal Gene Transfer.