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Home >> Genetics Dictionary >>Horizontal Gene Transfer
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Horizontal gene transfer
A key source of genetic variation is exchange of genetic material among individuals. Genetic exchange among closely related individuals is common in nature, and occurs in prokaryotes via conjugation and other processes, and in eukaryotes during sexual reproduction. When these same processes occur among individuals that are more distantly related and would not typically exchange genetic material, they are referred to as hybridization. But occasionally genetic material is exchanged among organisms that are very distantly related.
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This phenomenon, termed horizontal (or lateral) gene transfer, occurs relatively rarely, and was long presumed not to be important in evolution. However, as increasing amounts of information from deoxyribonucleic acid (DNA) sequences have become available, it has become clear that horizontal gene transfer is a significant part of evolution in nature.
Phylogenetic Analysis
Evidence of gene transfer can be found by way of comparative study of molecular phylogenies, which rely on the fact that when a mutation occurs in an individual's germ line its descendants can inherit the resulting variant sequence. Thus the descendants of the individual that underwent mutation can be recognized by their possession of a particular sequence variant. Over time, many mutations occur in any phylogenetic lineage; molecular phylogenetic analysis uses computer modeling to estimate the evolutionary relationships by reconstructing the history of mutation within the lineage.
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Because molecular phylogenetic analysis of gene sequences relies on the comparison of the same (homologous) gene from many individuals, each such phylogeny is really the phylogeny of a particular gene.
If molecular phylogenies are determined for two or more genes from the same group of organisms, one would expect these genes to have the same phylogenetic history (except, of course, for studies within a single species). In most cases, this is what is observed; phylogenetic analyses of multiple genes produce congruent phylogenies. However, there are several known cases where different genes seem to have different evolutionary histories, and it is among these that evidence of horizontal gene transfer is to be sought.
Incongruence among gene phylogenies does not necessarily indicate gene transfer. In some cases the sequences do not contain enough information for reliable phylogenetic analysis.
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In other cases the analyses are flawed because the analytical method used makes assumptions that are inappropriate for the data, or because nonhomologous genes have been included in the study. But in cases where these possibilities can be excluded, the best explanation for incongruent gene phylogenies is horizontal gene transfer. Ideally one would know the true phylogeny of the organisms in question.If this were the case, then identification of which conflicting gene phylogenies did not match that phylogeny would be possible. Because the true organismal phylogeny is rarely known, most studies look for a group of gene phylogenies that agree, and assume that these represent the organismal phylogeny. The discordant gene or genes are then assumed to have undergone gene transfer. If the putative transferred gene closely resembles the homolog from an unrelated organism, the hypothesis of gene transfer is strongly supported.
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| Codon Usage Patterns
Although phylogenetic analysis provides a powerful way to study horizontal gene transfer, there is the disadvantage that it requires examining several genes from a number of organisms. This can be difficult, particularly if some of the organisms involved have not been well studied with molecular methods. Another way to identify genes that have undergone horizontal transfer is to find regions of the genome that seem to be out of place; that is, they have characteristics that are atypical of the genome in which they reside. This approach provides information that complements that from phylogenetic analysis, and has the advantage that it is possible to examine every gene within a genome and assign to the gene likelihood that it has undergone recent transfer. From this information it is possible to make an estimate of the frequency with which horizontal gene transfer has occurred.
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Codon Usage Patterns
Although phylogenetic analysis provides a powerful way to study horizontal gene transfer, there is the disadvantage that it requires examining several genes from a number of organisms. This can be difficult, particularly if some of the organisms involved have not been well studied with molecular methods. Another way to identify genes that have undergone horizontal transfer is to find regions of the genome that seem to be out of place; that is, they have characteristics that are atypical of the genome in which they reside. This approach provides information that complements that from phylogenetic analysis, and has the advantage that it is possible to examine every gene within a genome and assign to the gene likelihood that it has undergone recent transfer. From this information it is possible to make an estimate of the frequency with which horizontal gene transfer has occurred.
Codon Usage Patterns
Although phylogenetic analysis provides a powerful way to study horizontal gene transfer, there is the disadvantage that it requires examining several genes from a number of organisms. This can be difficult, particularly if some of the organisms involved have not been well studied with molecular methods. Another way to identify genes that have undergone horizontal transfer is to find regions of the genome that seem to be out of place; that is, they have characteristics that are atypical of the genome in which they reside. This approach provides information that complements that from phylogenetic analysis, and has the advantage that it is possible to examine every gene within a genome and assign to the gene likelihood that it has undergone recent transfer. From this information it is possible to make an estimate of the frequency with which horizontal gene transfer has occurred.
Codon Usage Patterns
Although phylogenetic analysis provides a powerful way to study horizontal gene transfer, there is the disadvantage that it requires examining several genes from a number of organisms. This can be difficult, particularly if some of the organisms involved have not been well studied with molecular methods. Another way to identify genes that have undergone horizontal transfer is to find regions of the genome that seem to be out of place; that is, they have characteristics that are atypical of the genome in which they reside. This approach provides information that complements that from phylogenetic analysis, and has the advantage that it is possible to examine every gene within a genome and assign to the gene likelihood that it has undergone recent transfer. From this information it is possible to make an estimate of the frequency with which horizontal gene transfer has occurred.
Codon Usage Patterns
Although phylogenetic analysis provides a powerful way to study horizontal gene transfer, there is the disadvantage that it requires examining several genes from a number of organisms. This can be difficult, particularly if some of the organisms involved have not been well studied with molecular methods. Another way to identify genes that have undergone horizontal transfer is to find regions of the genome that seem to be out of place; that is, they have characteristics that are atypical of the genome in which they reside. This approach provides information that complements that from phylogenetic analysis, and has the advantage that it is possible to examine every gene within a genome and assign to the gene likelihood that it has undergone recent transfer. From this information it is possible to make an estimate of the frequency with which horizontal gene transfer has occurred.
To make these calculations, one examines the patterns of base composition and codon usage within the genome. These patterns are quite variable, and are generally characteristic of an organism, although some variation is found within genomes as well. Base composition refers to the relative quantities of each nucleotide in the DNA. There is a typical or background base composition for each major region of a genome, probably because of biases in the mutation-repair mechanisms and variation in the nucleotide precursor pools within the cell. The base composition is often different in genes than in intergenic regions, which are under weaker selective pressures and consequently are more free to adopt the background base composition for the genome. Layered on top of base compositional patterns are patterns of codon usage (the relative frequency with which each of the 64 codons is used in proteincoding genes).
The genetic code is degenerate (includes redundancy), with 64 codons to represent only 20 amino acids, and most amino acids can be encoded by more than one codon.
These synonymous codons are not typically used with equal frequency. Rather, each organism has a distinctive pattern of codon usage. Because these patterns of base composition and codon usage, often referred to simply as codon usage, are characteristic of the genome, they can be used as markers for the origin of each gene. Genes that are native to the genome have the characteristic codon usage for that genome. Genes that have recently undergone horizontal gene transfer from another organism have the codon usage characteristic of the donor genome. However, once a transferred gene is resident in its new genome, when mutations occur, replacements reflect the codon usage- biases characteristic of that genome. Thus, over time the codon usage of a transferred gene tends to change to resemble its new home, and consequently codon usage is useful only for detecting relatively recently transferred genes.
Many individual genes that have undergone horizontal gene transfer have now been identified in both prokaryotes and eukaryotes.
Fig Hierarchical classification. The branching tree on the left represents the history of specification within the group, with the present day populations depicted at the tip of each branch and their classification shown to the right. The hierarchical clustering of species reflects the history of specification.
| Genus A |
Genus B |
| Lineage 1 and 4 |
Species 3 |
| Species 1 |
Species 3 |
| Species 4 |
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| Lineage 2 and 5 |
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| Species 2 |
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| Species 5 |
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Some of the mast thoroughly documented cases of horizontal gene transfer involve the gene rbcL, which encodes the large subunit of ribulase-1,5-bisphophate carboxylase/ oxygenase (often called rubisco), a key enzyme in carbon fixation during photosynthesis by plant chloroplasts and their cyanobacterial relatives, as well as by photosynthetic proteobacteria.
Rubisco genes have had a camplex evolutionary history, and have undergone both gene duplication and horizontal gene transfer. Similar patterns have been identified in genes involved with adenosine triphosphate (ATP) synthesis, nitrogen fixation, and transfer ribonucleic acid (tRNA) synthesis, to name just a few. In a study of the relationship between prokaryotes and eukaryotes, researchers used molecular phylogenetic approaches to study the evolution of aver 60 protein-coding genes and found a highly complex pattern that suggests substantial horizontal gene transfer. This has led researchers to further investigate hierarchical classification, particularly at higher taxonomic levels.
Hierarchical classification
Horizontal gene transfer could substantially affect the concept of organismal phylogeny. Because all life is thought to be descended from a common ancestor, the history of speciation provides the basis far a natural classification of all living things (see illus.).
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