The genomes of living organisms are full of useful genes that govern traits such as hair color and behavior. But a large part of genomes are made up of DNA sequences that do not code for any traits. A closer look reveals the presence of some interesting elements, like the mobile transposons.
Transposons, being a class of mobile genetic elements, are, in the very strictest sense, DNA sequences that are capable of “moving around" a genome. The general structure of a simple transposable element consists of a central region of DNA flanked by inverted repeats, or the same sequence that runs in opposite directions on opposite sides of the DNA strands. The central region of some more complex transposable elements is sometimes flanked by short, direct repeats, which are then flanked by the inverted repeats. These mobile elements can be anywhere from a few hundred base pairs long to a few thousand; they are very abundant throughout the genomes of all living things, with some scientists claiming that they make up at least 10% of the genomes of eukaryotes. They were first discovered in maize, or Indian corn, by Dr. Barbara McClintock in the 1950s; she received the Nobel Prize in Physiology or Medicine for her work, in 1983.
There is some debate as to how many different “groups" of transposons there are, so in this article we are going to make things simple. We will look at two main types of transposable elements: DNA transposons and retrotransposons.
Retrotransposons, sometimes referred to as Class I mobile genetic elements, operate by first transcribing a copy of themselves into RNA and then using the enzyme reverse transcriptase to transcribe themselves back into DNA; this reverse transcribed DNA is then inserted into a new location. The reverse transcriptase is often encoded by the element itself. Many readers will notice a striking similarity with retroviruses, of which HIV is the most well known. Indeed, retroviruses work in a surprisingly similar manner to retrotransposons; the main difference between the two elements is that retroviruses also encode a variety of other viral proteins, some which allow the virus to survive outside the host. Retrotransposons cannot survive outside the host genome.
Within the category of retrotransposons, researchers have found some elements that are similar to retroviruses, called viral retrotransposons, which possess long terminal repeats, or LTRs, as well as elements called LINES, which do not have LTRs. There are some retrotransposons, furthermore, that do not themselves encode for reverse transcriptase; it is thought that these elements take advantage of the enzyme encoded by other retrotransposons.
Most DNA transposons, sometimes referred to as Class II mobile genetic elements, actually use two enzymes, transposase and integrase, to move from one location in the genome to another; they are literally “cut" out of their location and “pasted" into a new one. This type of transposition does not involve RNA. The enzymes may recognize specific sequences for insertion, though many types of enzyme can actually bind to virtually any sequence, allowing the element to be inserted anywhere. At the site where the transposon is to be inserted, the DNA is cut in what’s called a “staggered" manner to create “sticky ends"; what this means is that nucleotides are left without corresponding paired bases. Once the transposon is inserted into the target site, a DNA polymerase adds the missing nucleotides. This filling in of the gaps leads to duplication of short DNA sequences flanking the transposon and this has been hypothesized as a mechanism behind gene duplication. Finally, some DNA transposons actually will replicate themselves, with the copy then being inserted into the target site.
Just as occurs with retrotransposons, there have been cases observed in which DNA transposable elements have lost the enzymes necessary for transposition. They continue to be able to move thanks to the presence of enzymes encoded by other mobile elements. Besides the enzymes important for transposition, some bacterial transposons actually carry genes that are unrelated to movement and that confer an advantage; these are the genes responsible for the rapid spread of antibiotic resistance among bacteria.
So Are Transposons Good or Bad?
The movement of transposable elements can actually impact the phenotype of an organism and the amount of DNA in its genome. The replication of sequences to be inserted into new locations, as well as the filling in of gaps created by transposition, often increase the amount of genetic information in a genome.
On phenotypes, there can be multiple effects:
If transposons insert themselves into a coding region or into a regulatory sequence, they will most probably render that gene inactive.
- Upon leaving a site, the gap that is left by a transposon will need to be repaired; this repair, often, will cause genetic mutations in the original gene and render it inactive.
Sequences that are repeated multiple times lead to unequal crossing over and chromosomal abnormalities.
- A number of diseases in the human genome have been linked to transposons, such as Hemophilia A and B, Severe Combined Immunodeficiency, Porphyria, predisposition to cancer, and Duchenne Muscular Dystrophy.
Despite these negative aspects, there can be positive impacts of transposable elements:
- Sometimes non-transposon, coding, DNA gets carried along with mobile elements during transposition; this could lead to the duplication of beneficial genes or the creation of new genes.
- Sometimes genetic mutations caused by transposons may modify regulatory sequences and this could change the pattern of expression of a gene or its timing or the amount of gene produced, which could lead to some new, beneficial characteristics.
The rate of transposition has actually been observed to increase in some cases under conditions of stress. This higher rate of transposition could cause genetic mutations leading to new traits, which would allow an organism to better adapt to changing environmental conditions.
- Transposons have also come in handy as tools for scientists who wish to create transgenic organisms or modify an organism’s DNA for research purposes.
Molecular Biology of the Cell (Alberts et al., 1994)
Principles of Genetics (Tamarin, 1999)
Cam et al. “Host genome surveillance for retrotransposons by transposon-derived proteins." Nature, 2008.