Transposon
Encyclopedia
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
that can move or transpose themselves to new positions within the genome
Genome
In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....
of a single cell
Cell (biology)
The cell is the basic structural and functional unit of all known living organisms. It is the smallest unit of life that is classified as a living thing, and is often called the building block of life. The Alberts text discusses how the "cellular building blocks" move to shape developing embryos....
. The mechanism of transposition can be either "copy and paste" or "cut and paste". Transposition can create phenotypically significant mutation
Mutation
In molecular biology and genetics, mutations are changes in a genomic sequence: the DNA sequence of a cell's genome or the DNA or RNA sequence of a virus. They can be defined as sudden and spontaneous changes in the cell. Mutations are caused by radiation, viruses, transposons and mutagenic...
s and alter the cell's genome size
Genome size
Genome size is the total amount of DNA contained within one copy of a single genome. It is typically measured in terms of mass in picograms or less frequently in Daltons or as the total number of nucleotide base pairs typically in megabases . One picogram equals 978 megabases...
. Barbara McClintock
Barbara McClintock
Barbara McClintock , the 1983 Nobel Laureate in Physiology or Medicine, was an American scientist and one of the world's most distinguished cytogeneticists. McClintock received her PhD in botany from Cornell University in 1927, where she was a leader in the development of maize cytogenetics...
's discovery of these jumping genes early in her career earned her a Nobel prize
Nobel Prize
The Nobel Prizes are annual international awards bestowed by Scandinavian committees in recognition of cultural and scientific advances. The will of the Swedish chemist Alfred Nobel, the inventor of dynamite, established the prizes in 1895...
in 1983.
TEs make up a large fraction of the C-value
C-value
The term C-value refers to the amount of DNA contained within a haploid nucleus or one half the amount in a diploid somatic cell of a eukaryotic organism, expressed in picograms...
of eukaryotic
Eukaryote
A eukaryote is an organism whose cells contain complex structures enclosed within membranes. Eukaryotes may more formally be referred to as the taxon Eukarya or Eukaryota. The defining membrane-bound structure that sets eukaryotic cells apart from prokaryotic cells is the nucleus, or nuclear...
cells. They are often considered "junk DNA". In Oxytricha
Stichotrich
The stichotrichs are a group of ciliate protozoa, included among the spirotrichs. Like the hypotrichs, with which they were originally classified, they have body cilia fused into cirri, but these are mostly arranged into rows, running along the ventral surface or edges of the cell. Most...
, which has a unique genetic system, they play a critical role in its development. They are also very useful to researchers as a means to alter DNA inside a living organism.
Classification
Transposable elements are only one of several types of mobile genetic elementsMobile genetic elements
Mobile genetic elements are a type of DNA that can move around within the genome. They include:*Transposons **Retrotransposons**DNA transposons**Insertion sequences*Plasmids...
. They are assigned to one of two classes according to their mechanism of transposition, which can be described as either "copy and paste" (for class I TEs) or "cut and paste" (for class II TEs).
Class I (Retrotransposons):
They copy themselves in two stages, first from DNA to RNA
RNA
Ribonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....
by transcription
Transcription (genetics)
Transcription is the process of creating a complementary RNA copy of a sequence of DNA. Both RNA and DNA are nucleic acids, which use base pairs of nucleotides as a complementary language that can be converted back and forth from DNA to RNA by the action of the correct enzymes...
, then from RNA back to DNA by reverse transcription. The DNA copy is then inserted into the genome in a new position. Reverse transcription is catalyzed by a reverse transcriptase
Reverse transcriptase
In the fields of molecular biology and biochemistry, a reverse transcriptase, also known as RNA-dependent DNA polymerase, is a DNA polymerase enzyme that transcribes single-stranded RNA into single-stranded DNA. It also helps in the formation of a double helix DNA once the RNA has been reverse...
, which is often coded by the TE itself. Retrotransposons behave very similarly to retrovirus
Retrovirus
A retrovirus is an RNA virus that is duplicated in a host cell using the reverse transcriptase enzyme to produce DNA from its RNA genome. The DNA is then incorporated into the host's genome by an integrase enzyme. The virus thereafter replicates as part of the host cell's DNA...
es, such as HIV
HIV
Human immunodeficiency virus is a lentivirus that causes acquired immunodeficiency syndrome , a condition in humans in which progressive failure of the immune system allows life-threatening opportunistic infections and cancers to thrive...
.
There are three main orders of retrotransposons (other orders are less abundant):
- those with LTRs: encode reverse transcriptase, have long terminal repeatLong terminal repeatLong terminal repeats are sequences of DNA that repeat hundreds or thousands of times. They are found in retroviral DNA and in retrotransposons, flanking functional genes...
s (LTRs), similar to retroviruses; - LINEs: encode reverse transcriptase, lack LTRs, transcribed by RNA polymerase IIRNA polymerase IIRNA polymerase II is an enzyme found in eukaryotic cells. It catalyzes the transcription of DNA to synthesize precursors of mRNA and most snRNA and microRNA. A 550 kDa complex of 12 subunits, RNAP II is the most studied type of RNA polymerase...
; - SINEs: do not code for reverse transcriptase, transcribed by RNA polymerase IIIRNA polymerase IIIRNA polymerase III transcribes DNA to synthesize ribosomal 5S rRNA, tRNA and other small RNAs. The genes transcribed by RNA Pol III fall in the category of "housekeeping" genes whose expression is required in all cell types and most environmental conditions...
.
Retroviruses can be considered as TEs. Indeed, after entering a host cell and converting their RNA into DNA, retrovirus
Retrovirus
A retrovirus is an RNA virus that is duplicated in a host cell using the reverse transcriptase enzyme to produce DNA from its RNA genome. The DNA is then incorporated into the host's genome by an integrase enzyme. The virus thereafter replicates as part of the host cell's DNA...
es integrate this DNA into the DNA of the host cell. The integrated DNA form (provirus) of the retrovirus is viewed as a particularly specialized form of eukaryotic retrotransposon, which is able to encode RNA intermediates that usually can leave the host cells and infect other cells. The transposition cycle of retroviruses also has similarities to that of prokaryotic TEs. The similarities suggest a distant familial relationship between these two TEs types.
Class II (DNA transposons):
By contrast, the cut-and-paste transposition mechanism of class II TEs does not involve an RNA intermediate. The transpositions are catalyzed by various types of transposase
Transposase
Transposase is an enzyme that binds to the ends of a transposon and catalyzes the movement of the transposon to another part of the genome by a cut and paste mechanism or a replicative transposition mechanism....
enzymes. Some transposases can bind non-specifically to any target site, while others bind to specific sequence targets. The transposase makes a staggered cut at the target site producing sticky ends, cuts out the DNA transposon and ligates it into the target site. A DNA polymerase
DNA polymerase
A DNA polymerase is an enzyme that helps catalyze in the polymerization of deoxyribonucleotides into a DNA strand. DNA polymerases are best known for their feedback role in DNA replication, in which the polymerase "reads" an intact DNA strand as a template and uses it to synthesize the new strand....
fills in the resulting gaps from the sticky ends and DNA ligase
DNA ligase
In molecular biology, DNA ligase is a specific type of enzyme, a ligase, that repairs single-stranded discontinuities in double stranded DNA molecules, in simple words strands that have double-strand break . Purified DNA ligase is used in gene cloning to join DNA molecules together...
closes the sugar-phosphate backbone. This results in target site duplication and the insertion sites of DNA transposons may be identified by short direct repeats (a staggered cut in the target DNA filled by DNA polymerase) followed by inverted repeats (which are important for the TE excision by transposase). The duplications at the target site can result in gene duplication
Gene duplication
Gene duplication is any duplication of a region of DNA that contains a gene; it may occur as an error in homologous recombination, a retrotransposition event, or duplication of an entire chromosome.The second copy of the gene is often free from selective pressure — that is, mutations of it have no...
, which plays an important role in evolution
Evolution
Evolution is any change across successive generations in the heritable characteristics of biological populations. Evolutionary processes give rise to diversity at every level of biological organisation, including species, individual organisms and molecules such as DNA and proteins.Life on Earth...
.
Not all DNA transposons transpose through a cut-and-paste mechanism. In some cases a replicative transposition
Replicative transposition
Replicative transposition is a mechanism of transposition in molecular biology, proposed by James A. Shapiro in 1979, in which the transposable element is duplicated during the reaction, so that the transposing entity is a copy of the original element...
is observed in which transposon replicates itself to a new target site (e.g. Helitron (biology)
Helitron (biology)
A helitron is a transposon found in eukaryotes that is thought to replicate by a rolling-circle mechanism....
).
Cut-and-paste TEs may be duplicated if transposition takes place during S phase
S phase
S-phase is the part of the cell cycle in which DNA is replicated, occurring between G1 phase and G2 phase. Precise and accurate DNA replication is necessary to prevent genetic abnormalities which often lead to cell death or disease. Due to the importance, the regulatory pathways that govern this...
of the cell cycle
Cell cycle
The cell cycle, or cell-division cycle, is the series of events that takes place in a cell leading to its division and duplication . In cells without a nucleus , the cell cycle occurs via a process termed binary fission...
when the "donor" site has already been replicated, but the "target" site has not.
Both classes of TEs may lose their ability to synthesise reverse transcriptase or transposase through mutation, yet continue to jump through the genome because other TEs are still producing the necessary enzymes. Hence, they can be classified as either "autonomous" or "non-autonomous". For instance for the class II TEs, the autonomous ones have an intact gene that encodes an active transposase enzyme; the TE does not need another source of transposase for its transposition. In contrast, non-autonomous elements encode defective polypeptides and accordingly require transposase from another source. When a TE is used as a genetic tool, the transposase is supplied by the investigator, often from an expression cassette
Expression cassette
An expression cassette is made up of one or more genes and the sequences controlling their expression. Three components comprise an expression cassette: a promoter sequence, an open reading frame, and a 3' untranslated region that, in eukaryotes, usually contains a polyadenylation site. The...
within a plasmid
Plasmid
In microbiology and genetics, a plasmid is a DNA molecule that is separate from, and can replicate independently of, the chromosomal DNA. They are double-stranded and, in many cases, circular...
.
Examples
- The first TEs were discovered in maizeMaizeMaize known in many English-speaking countries as corn or mielie/mealie, is a grain domesticated by indigenous peoples in Mesoamerica in prehistoric times. The leafy stalk produces ears which contain seeds called kernels. Though technically a grain, maize kernels are used in cooking as a vegetable...
(Zea mays), by Barbara McClintockBarbara McClintockBarbara McClintock , the 1983 Nobel Laureate in Physiology or Medicine, was an American scientist and one of the world's most distinguished cytogeneticists. McClintock received her PhD in botany from Cornell University in 1927, where she was a leader in the development of maize cytogenetics...
in 1948, for which she was awarded a Nobel PrizeNobel PrizeThe Nobel Prizes are annual international awards bestowed by Scandinavian committees in recognition of cultural and scientific advances. The will of the Swedish chemist Alfred Nobel, the inventor of dynamite, established the prizes in 1895...
in 1983. She noticed insertions, deletionsGenetic deletionIn genetics, a deletion is a mutation in which a part of a chromosome or a sequence of DNA is missing. Deletion is the loss of genetic material. Any number of nucleotides can be deleted, from a single base to an entire piece of chromosome...
, and translocationsChromosomal translocationIn genetics, a chromosome translocation is a chromosome abnormality caused by rearrangement of parts between nonhomologous chromosomes. A gene fusion may be created when the translocation joins two otherwise separated genes, the occurrence of which is common in cancer. It is detected on...
, caused by these elements. These changes in the genome could, for example, lead to a change in the color of corn kernels. About 85% of the genome of maize consists in TEs. The Ac/Ds system described by McClintock are class II TEs. Transposition of Ac in tobacco has been demonstrated by B. Baker (Plant Transposable Elements, pp 161-174, 1988, Plenum Publishing Corp., ed. Nelson).
- One family of TEs in the fruit fly Drosophila melanogasterDrosophila melanogasterDrosophila melanogaster is a species of Diptera, or the order of flies, in the family Drosophilidae. The species is known generally as the common fruit fly or vinegar fly. Starting from Charles W...
are called P elements. They seem to have first appeared in the speciesSpeciesIn biology, a species is one of the basic units of biological classification and a taxonomic rank. A species is often defined as a group of organisms capable of interbreeding and producing fertile offspring. While in many cases this definition is adequate, more precise or differing measures are...
only in the middle of the twentieth century. Within 50 years, they have spread through every populationPopulationA population is all the organisms that both belong to the same group or species and live in the same geographical area. The area that is used to define a sexual population is such that inter-breeding is possible between any pair within the area and more probable than cross-breeding with individuals...
of the species. Gerald M. RubinGerald M. RubinGerald M. Rubin is an American biologist, notable for pioneering the use of transposable P elements in genetics, and for leading the public project to sequence the Drosophila melanogaster genome. Related to his genomics work, Rubin's lab is notable for development of genomics tools and...
and Allan C. SpradlingAllan C. SpradlingAllan C. Spradling is an American scientist and principal investigator at the Carnegie Institution for Science and the Howard Hughes Medical Institute who studies egg development in the model organism, Drosophila melanogaster, a fruit fly...
pioneered technology to use artificial P elements to insert genes into Drosophila by injecting the embryoEmbryoAn embryo is a multicellular diploid eukaryote in its earliest stage of development, from the time of first cell division until birth, hatching, or germination...
.
- Transposons in bacteriaBacteriaBacteria are a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals...
usually carry an additional gene for function other than transposition---often for antibiotic resistanceAntibiotic resistanceAntibiotic resistance is a type of drug resistance where a microorganism is able to survive exposure to an antibiotic. While a spontaneous or induced genetic mutation in bacteria may confer resistance to antimicrobial drugs, genes that confer resistance can be transferred between bacteria in a...
. In bacteria, transposons can jump from chromosomalChromosomeA chromosome is an organized structure of DNA and protein found in cells. It is a single piece of coiled DNA containing many genes, regulatory elements and other nucleotide sequences. Chromosomes also contain DNA-bound proteins, which serve to package the DNA and control its functions.Chromosomes...
DNA to plasmidPlasmidIn microbiology and genetics, a plasmid is a DNA molecule that is separate from, and can replicate independently of, the chromosomal DNA. They are double-stranded and, in many cases, circular...
DNA and back, allowing for the transfer and permanent addition of genes such as those encoding antibiotic resistance (multi-antibiotic resistantMultidrug resistanceMultiple drug resistance or Multidrug resistance is a condition enabling a disease-causing organism to resist distinct drugs or chemicals of a wide variety of structure and function targeted at eradicating the organism...
bacterial strains can be generated in this way). Bacterial transposons of this type belong to the Tn family. When the transposable elements lack additional genes, they are known as insertion sequenceInsertion sequenceAn insertion sequence is a short DNA sequence that acts as a simple transposable element...
s.
- The most common form of transposon in humanHumanHumans are the only living species in the Homo genus...
s is the Alu sequenceAlu sequenceAn Alu element is a short stretch of DNA originally characterized by the action of the Alu restriction endonuclease. Alu elements of different kinds occur in large numbers in primate genomes. In fact, Alu elements are the most abundant mobile elements in the human genome. They are derived from the...
. It is approximately 300 bases long and can be found between 300,000 and a million times in the human genomeHuman genomeThe human genome is the genome of Homo sapiens, which is stored on 23 chromosome pairs plus the small mitochondrial DNA. 22 of the 23 chromosomes are autosomal chromosome pairs, while the remaining pair is sex-determining...
.
- Mariner-like elements are another prominent class of transposons found in multiple species including humans. The Mariner transposon was first discovered by Jacobson and Hartl in Drosophila. This Class II transposable element is known for its uncanny ability to be transmitted horizontally in many species. There are an estimated 14 thousand copies of Mariner in the human genome comprising 2.6 million base pairs. These characteristics of the Mariner transposon have inspired the science fiction novel titled, "The Mariner ProjectThe Mariner ProjectThe Mariner Project is a science fiction novel written by Bob Marr. The author is a molecular virologist working on gene therapy applications of viral vectors to diseases such as Alzheimer’s disease....
".
- Mu phageMu phageBacteriophage Mu or phage Mu is a temperate bacteriophage, a type of virus that infects bacteria.-Replication:It uses DNA-based transposition to integrate its genome into the genome of the host cell that it is infecting. It can then use transposition to initiate its viral DNA replication...
transposition is the best known example of replicative transpositionReplicative transpositionReplicative transposition is a mechanism of transposition in molecular biology, proposed by James A. Shapiro in 1979, in which the transposable element is duplicated during the reaction, so that the transposing entity is a copy of the original element...
. Its transposition mechanism is somewhat similar to a homologous recombinationHomologous recombinationHomologous recombination is a type of genetic recombination in which nucleotide sequences are exchanged between two similar or identical molecules of DNA. It is most widely used by cells to accurately repair harmful breaks that occur on both strands of DNA, known as double-strand breaks...
.
- The five distinct yeast (Saccharomyces cerevisiaeSaccharomyces cerevisiaeSaccharomyces cerevisiae is a species of yeast. It is perhaps the most useful yeast, having been instrumental to baking and brewing since ancient times. It is believed that it was originally isolated from the skin of grapes...
) retrotransposon families: Ty1, Ty2, Ty3, Ty4 and Ty5
- A helitronHelitron (biology)A helitron is a transposon found in eukaryotes that is thought to replicate by a rolling-circle mechanism....
is a TE found in eukaryotes that are thought to replicate by a rolling-circleRolling circle replicationRolling circle replication describes a process of unidirectional nucleic acid replication that can rapidly synthesize multiple copies of circular molecules of DNA or RNA, such as plasmids, the genomes of bacteriophages, and the circular RNA genome of viroids...
mechanism.
In disease
TEs are mutagenMutagen
In genetics, a mutagen is a physical or chemical agent that changes the genetic material, usually DNA, of an organism and thus increases the frequency of mutations above the natural background level. As many mutations cause cancer, mutagens are therefore also likely to be carcinogens...
s. They can damage the genome of their host cell in different ways :
- a transposon or a retroposon that inserts itself into a functional gene will most likely disable that gene;
- after a DNA transposon leaves a gene, the resulting gap will probably not be repaired correctly;
- multiple copies of the same sequence, such as Alu sequenceAlu sequenceAn Alu element is a short stretch of DNA originally characterized by the action of the Alu restriction endonuclease. Alu elements of different kinds occur in large numbers in primate genomes. In fact, Alu elements are the most abundant mobile elements in the human genome. They are derived from the...
s can hinder precise chromosomalChromosomeA chromosome is an organized structure of DNA and protein found in cells. It is a single piece of coiled DNA containing many genes, regulatory elements and other nucleotide sequences. Chromosomes also contain DNA-bound proteins, which serve to package the DNA and control its functions.Chromosomes...
pairing during mitosisMitosisMitosis is the process by which a eukaryotic cell separates the chromosomes in its cell nucleus into two identical sets, in two separate nuclei. It is generally followed immediately by cytokinesis, which divides the nuclei, cytoplasm, organelles and cell membrane into two cells containing roughly...
and meiosisMeiosisMeiosis is a special type of cell division necessary for sexual reproduction. The cells produced by meiosis are gametes or spores. The animals' gametes are called sperm and egg cells....
, resulting in unequal crossoverChromosomal crossoverChromosomal crossover is an exchange of genetic material between homologous chromosomes. It is one of the final phases of genetic recombination, which occurs during prophase I of meiosis in a process called synapsis. Synapsis begins before the synaptonemal complex develops, and is not completed...
s, one of the main reasons for chromosome duplication.
Diseases that are often caused by TEs include hemophilia A and B, severe combined immunodeficiency
Severe combined immunodeficiency
Severe combined immunodeficiency , is a genetic disorder in which both "arms" of the adaptive immune system are impaired due to a defect in one of several possible genes. SCID is a severe form of heritable immunodeficiency...
, porphyria
Porphyria
Porphyrias are a group of inherited or acquired disorders of certain enzymes in the heme bio-synthetic pathway . They are broadly classified as acute porphyrias and cutaneous porphyrias, based on the site of the overproduction and accumulation of the porphyrins...
, predisposition to cancer
Cancer
Cancer , known medically as a malignant neoplasm, is a large group of different diseases, all involving unregulated cell growth. In cancer, cells divide and grow uncontrollably, forming malignant tumors, and invade nearby parts of the body. The cancer may also spread to more distant parts of the...
, and Duchenne muscular dystrophy
Duchenne muscular dystrophy
Duchenne muscular dystrophy is a recessive X-linked form of muscular dystrophy, which results in muscle degeneration, difficulty walking, breathing, and death. The incidence is 1 in 3,000 boys. Females and males are affected, though females are rarely affected and are more often carriers...
.
Additionally, many TEs contain promoters which drive transcription
Transcription (genetics)
Transcription is the process of creating a complementary RNA copy of a sequence of DNA. Both RNA and DNA are nucleic acids, which use base pairs of nucleotides as a complementary language that can be converted back and forth from DNA to RNA by the action of the correct enzymes...
of their own transposase
Transposase
Transposase is an enzyme that binds to the ends of a transposon and catalyzes the movement of the transposon to another part of the genome by a cut and paste mechanism or a replicative transposition mechanism....
. These promoters can cause aberrant expression of linked genes, causing disease or mutant
Mutant
In biology and especially genetics, a mutant is an individual, organism, or new genetic character, arising or resulting from an instance of mutation, which is a base-pair sequence change within the DNA of a gene or chromosome of an organism resulting in the creation of a new character or trait not...
phenotypes.
Rate of transposition, induction and defense
One study estimated the rate of transposition of a particular retrotransposon, the Ty1 element in Saccharomyces cerevisiaeSaccharomyces cerevisiae
Saccharomyces cerevisiae is a species of yeast. It is perhaps the most useful yeast, having been instrumental to baking and brewing since ancient times. It is believed that it was originally isolated from the skin of grapes...
. Using several assumptions, the rate of successful transposition event per single Ty1 element came out to be about once every few months to once every few years.
Cells defend against the proliferation of TEs in a number of ways. These include piRNA
Piwi-interacting RNA
Piwi-interacting RNA is the largest class of small non-coding RNA molecules that is expressed in animal cells. piRNAs form RNA-protein complexes through interactions with piwi proteins...
s and siRNA
Sírna
Sírna Sáeglach , son of Dian mac Demal, son of Demal mac Rothechtaid, son of Rothechtaid mac Main, was, according to medieval Irish legend and historical tradition, a High King of Ireland...
s which silence TEs after they have been transcribed.
Some TEs contain heat-shock like
Heat shock protein
Heat shock proteins are a class of functionally related proteins involved in the folding and unfolding of other proteins. Their expression is increased when cells are exposed to elevated temperatures or other stress. This increase in expression is transcriptionally regulated...
promoters and their rate of transposition increases if the cell is subjected to stress, thus increasing the mutation rate under these conditions, which might be beneficial to the cell.
Evolution
The evolution of TEs and their effect on genome evolution is currently a dynamic field of study.TEs are found in many major branches of life. They may have originated in the last universal common ancestor, or arisen independently multiple times, or perhaps arisen once and then spread to other kingdoms by horizontal gene transfer
Horizontal gene transfer
Horizontal gene transfer , also lateral gene transfer , is any process in which an organism incorporates genetic material from another organism without being the offspring of that organism...
. While some TEs may confer benefits on their hosts, most are regarded as selfish DNA
Selfish DNA
Selfish DNA refers to those sequences of DNA which, in their purest form, have two distinct properties: the DNA sequence spreads by forming additional copies of itself within the genome; and it makes no specific contribution to the reproductive success of its host organism.This idea was sketched...
parasites. In this way, they are similar to virus
Virus
A virus is a small infectious agent that can replicate only inside the living cells of organisms. Viruses infect all types of organisms, from animals and plants to bacteria and archaea...
es. Various viruses and TEs also share features in their genome structures and biochemical abilities, leading to speculation that they share a common ancestor.
Since excessive TE activity can destroy a genome, many organisms have developed mechanisms to inhibit this activity. Bacteria may undergo high rates of gene deletion as part of a mechanism to remove TEs and viruses from their genomes while eukaryotic
Eukaryote
A eukaryote is an organism whose cells contain complex structures enclosed within membranes. Eukaryotes may more formally be referred to as the taxon Eukarya or Eukaryota. The defining membrane-bound structure that sets eukaryotic cells apart from prokaryotic cells is the nucleus, or nuclear...
organism
Organism
In biology, an organism is any contiguous living system . In at least some form, all organisms are capable of response to stimuli, reproduction, growth and development, and maintenance of homoeostasis as a stable whole.An organism may either be unicellular or, as in the case of humans, comprise...
s use RNA interference
RNA interference
RNA interference is a process within living cells that moderates the activity of their genes. Historically, it was known by other names, including co-suppression, post transcriptional gene silencing , and quelling. Only after these apparently unrelated processes were fully understood did it become...
(RNAi) to inhibit TE activity. Nevertheless, some TEs generated large families often associated with speciation
Speciation
Speciation is the evolutionary process by which new biological species arise. The biologist Orator F. Cook seems to have been the first to coin the term 'speciation' for the splitting of lineages or 'cladogenesis,' as opposed to 'anagenesis' or 'phyletic evolution' occurring within lineages...
events.
Evolution has been particularly harsh on DNA transposons. In vertebrate animal cells nearly all >100,000 DNA transposons per genome have genes that encode inactive transposase polypeptides. In humans, all of the Tc1-like transposons are inactive. As a result the first DNA transposon used as a tool for genetic purposes, the Sleeping Beauty transposon system
Sleeping Beauty transposon system
The Sleeping Beauty transposon system is a synthetic DNA transposon that was constructed 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 their functions.-Mechanism of Action:The Sleeping...
, was a Tc1/mariner-like transposon that was resurrected from a long evolutionary sleep.
Interspersed Repeats
Interspersed repeat
Interspersed repetitive DNA is found in all eukaryotic genomes. Certain classes of these sequences propagate themselves by RNA mediated transposition, and they have been called retrotransposons. Interspersed repetitive DNA elements allow new genes to evolve. They do this by uncoupling similar DNA...
within genomes are created by transposition events accumulating over evolutionary time. Because interspersed repeats block gene conversion
Gene conversion
Gene conversion is an event in DNA genetic recombination, which occurs at high frequencies during meiotic division but which also occurs in somatic cells. It is a process by which DNA sequence information is transferred from one DNA helix to another DNA helix, whose sequence is altered.It is one...
, they protect novel gene sequences from being overwritten by similar gene sequences and thereby facilitate the development of new genes.
TEs may have been co-opted by the vertebrate immune system
Adaptive immune system
The adaptive immune system is composed of highly specialized, systemic cells and processes that eliminate or prevent pathogenic growth. Thought to have arisen in the first jawed vertebrates, the adaptive or "specific" immune system is activated by the “non-specific” and evolutionarily older innate...
as a means of producing antibody diversity: The V(D)J recombination
V(D)J recombination
VJ recombination, also known as somatic recombination, is a mechanism of genetic recombination in the early stages of immunoglobulin and T cell receptors production of the immune system...
system operates by a mechanism similar to that of some TEs.
TEs contain many type of genes- including those conferring antibiotic resistance and ability to transpose to conjugative plasmid. Some TEs also contain integrons(genetic elements that can capture and express genes from other sources) that contain integrase enzyme which can integrate gene cassettes. over 40 antibiotic resistance genes identified on cassettes: also virulance genes.
Applications
The first TE was discovered in the plant maizeMaize
Maize known in many English-speaking countries as corn or mielie/mealie, is a grain domesticated by indigenous peoples in Mesoamerica in prehistoric times. The leafy stalk produces ears which contain seeds called kernels. Though technically a grain, maize kernels are used in cooking as a vegetable...
(Zea mays, corn species), and is named dissociator (Ds). Likewise, the first TE to be molecularly isolated was from a plant (Snapdragon
SnapDragon
SnapDragon is a contemporary jazz band based in San Antonio, Texas. The group released their debut CD, "Stealing a Moment" on Humbug Records in 2008, and the 10-song CD soon broke the Top 100 in U.S radio airplay...
).
Appropriately, TEs have been an especially useful tool in plant molecular biology. Researchers use them as a means of mutagenesis. In this context, a TE jumps into a gene and produces a mutation. The presence of such a TE provides a straightforward means of identifying the mutant allele, relative to chemical mutagenesis methods.
Sometimes the insertion of a TE into a gene can disrupt that gene's function in a reversible manner, in a process called insertional mutagenesis
Insertional mutagenesis
Insertional mutagenesis is mutagenesis of DNA by the insertion of one or more bases.Insertional mutations can occur naturally, mediated by virus or transposon, or can be artificially created for research purposes in the lab.- Signature tagged mutagenesis :...
; transposase-mediated excision of the DNA transposon restores gene function. This produces plants in which neighboring cells have different genotype
Genotype
The genotype is the genetic makeup of a cell, an organism, or an individual usually with reference to a specific character under consideration...
s. This feature allows researchers to distinguish between genes that must be present inside of a cell in order to function (cell-autonomous) and genes that produce observable effects in cells other than those where the gene is expressed.
TEs are also a widely used tool for mutagenesis of most experimentally tractable organisms. The Sleeping Beauty transposon system
Sleeping Beauty transposon system
The Sleeping Beauty transposon system is a synthetic DNA transposon that was constructed 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 their functions.-Mechanism of Action:The Sleeping...
has been used extensively as an insertional tag for identifying cancer genes
The Tc1/mariner-class of TEs Sleeping Beauty transposon system
Sleeping Beauty transposon system
The Sleeping Beauty transposon system is a synthetic DNA transposon that was constructed 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 their functions.-Mechanism of Action:The Sleeping...
, awarded as the Molecule of the Year 2009 is active in mammalian cells and are being investigated for use in human gene therapy
Gene therapy
Gene therapy is the insertion, alteration, or removal of genes within an individual's cells and biological tissues to treat disease. It is a technique for correcting defective genes that are responsible for disease development...
.
See also
- Insertion sequenceInsertion sequenceAn insertion sequence is a short DNA sequence that acts as a simple transposable element...
- Intragenomic conflictIntragenomic conflictThe selfish gene theory postulates that natural selection will increase the frequency of those genes whose phenotypic effects ensure their successful replication...
- P element
- Tn10Tn10Tn 10 is a transposable element, which is a sequence of DNA that is capable of mediating its own movement through the DNA of host organisms. This fragment of DNA can move from position to position on the chromosome or plasmid by cut-and-paste transposition...
- Signature tagged mutagenesisSignature tagged mutagenesisSignature-tagged mutagenesis is a genetic technique used to study gene function. Recent advances in genome sequencing have allowed us to catalogue a large variety of organisms genomes, but the function of the genes they contain is still largely unknown...
- Evolution of sexual reproduction
External links
- Kimball's Biology Pages: Transposons
- A possible connection between aberrant reinsertions and lymphoma - New Scientist
- GMO Safety: Transposons - research projects and basic infos
- A wiki specially dedicated to transposable elements and their classification
- Repbase - a database of transposable element sequences
- RepeatMasker - a computer program used by computational biologists to annotate transposons in DNA sequences
- Use of the Sleeping Beauty Transposon System for Stable Gene Expression in Mouse Embryonic Stem Cells