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Encyclopedia > Transposon
A DNA composite transposon.
A DNA composite transposon.

Transposons are sequences of DNA that can move around to different positions within the genome of a single cell, a process called transposition. In the process, they can cause mutations and change the amount of DNA in the genome. Transposons are also called "jumping genes", and are examples of mobile genetic elements. Discovered by Barbara McClintock early in her career[1], the discovery earned her a Nobel prize in 1983. There are a variety of mobile genetic elements, and they can be grouped based on their mechanism of transposition. Class I mobile genetic elements, or retrotransposons, move in the genome by being transcribed to RNA and then back to DNA by reverse transcriptase, while class II mobile genetic elements move directly from one position to another within the genome using a transposase to "cut and paste" them within the genome. Transposons are very useful to researchers as a means to alter DNA inside of a living organism. Transposons make up a large fraction of genome sizes which is evident through the C-values of eukaryotic species. Image File history File links Composite_transposon. ... Image File history File links Composite_transposon. ... The structure of part of a DNA double helix Deoxyribonucleic acid, or DNA, is a nucleic acid molecule that contains the genetic instructions used in the development and functioning of all known living organisms. ... In biology the genome of an organism is the whole hereditary information of an organism that is encoded in the DNA (or, for some viruses, RNA). ... Drawing of the structure of cork as it appeared under the microscope to Robert Hooke from Micrographia which is the origin of the word cell being used to describe the smallest unit of a living organism Cells in culture, stained for keratin (red) and DNA (green) The cell is the... For linguistic mutation, see Apophony. ... Mobile genetic elements (MGE) are a type of DNA that can move around within the genome. ... Barbara McClintock (June 16, 1902 – September 2, 1992) was a pioneering American scientist and one of the worlds most distinguished cytogeneticists. ... The Nobel Prize (Swedish: ) was established in Alfred Nobels will in 1895, and it was first awarded in Physics, Chemistry, Physiology or Medicine, Literature, and Peace in 1901. ... Year 1983 (MCMLXXXIII) was a common year starting on Saturday (link displays the 1983 Gregorian calendar). ... Retrotransposons are genetic elements than can amplify themselves in a genome and are ubiquitous components of the DNA of many eukaryotic organisms. ... A micrograph of ongoing gene transcription of ribosomal RNA illustrating the growing primary transcripts. ... Left: An RNA strand, with its nitrogenous bases. ... In biochemistry, a reverse transcriptase, also known as RNA-dependent DNA polymerase, is a DNA polymerase enzyme that transcribes single-stranded RNA into double-stranded DNA. Normal transcription involves the synthesis of RNA from DNA, hence reverse transcription is the reverse of this. ... Transposase is an enzyme that binds to single-stranded DNA and can incorporate it into genomic DNA. Class I transposons encode a transposase which allows them to enable transposons to be cut from genomic DNA and be inserted at another location. ... Genome size refers to the total amount of DNA contained within one copy of a genome. ... The term C-value refers to the amount of DNA contained within a haploid nucleus (e. ... Kingdoms Animalia - Animals Fungi Plantae - Plants Chromalveolata Protista Alternative phylogeny Unikonta Opisthokonta Metazoa Choanozoa Eumycota Amoebozoa Bikonta Apusozoa Cabozoa Rhizaria Excavata Corticata Archaeplastida Chromalveolata Animals, plants, fungi, and protists are eukaryotes (IPA: ), organisms whose cells are organized into complex structures by internal membranes and a cytoskeleton. ...

Contents

Types of transposons

Transposons are classified into two classes based on their mechanism of transposition.


Class I: Retrotransposons

Main article: Retrotransposon

Retrotransposons work by copying themselves and pasting copies back into the genome in multiple places. Initially retrotransposons copy themselves to RNA (transcription) but, in addition to being transcribed, the RNA is copied into DNA by a reverse transcriptase (often coded by the transposon itself) and inserted back into the genome. Retrotransposons are genetic elements than can amplify themselves in a genome and are ubiquitous components of the DNA of many eukaryotic organisms. ... Left: An RNA strand, with its nitrogenous bases. ... A micrograph of ongoing gene transcription of ribosomal RNA illustrating the growing primary transcripts. ... The structure of part of a DNA double helix Deoxyribonucleic acid, or DNA, is a nucleic acid molecule that contains the genetic instructions used in the development and functioning of all known living organisms. ... In biochemistry, a reverse transcriptase, also known as RNA-dependent DNA polymerase, is a DNA polymerase enzyme that transcribes single-stranded RNA into double-stranded DNA. Normal transcription involves the synthesis of RNA from DNA, hence reverse transcription is the reverse of this. ...


Retrotransposons behave very similarly to retroviruses, such as HIV, giving a clue to the evolutionary origins of such viruses. Genera Alpharetrovirus Betaretrovirus Gammaretrovirus Deltaretrovirus Epsilonretrovirus Lentivirus Spumavirus A retrovirus is any virus belonging to the viral family Retroviridae. ... Species Human immunodeficiency virus 1 Human immunodeficiency virus 2 Human immunodeficiency virus (HIV) is a retrovirus that causes acquired immunodeficiency syndrome (AIDS, a condition in humans in which the immune system begins to fail, leading to life-threatening opportunistic infections). ... This article is about evolution in biology. ...


There are three main classes of Retrotransposons:

  • Viral: encode reverse transcriptase (to reverse transcribe RNA into DNA), have long terminal repeats (LTRs), similar to retroviruses
  • LINEs: encode reverse transcriptase, lack LTRs, transcribed by RNA polymerase II
  • Nonviral superfamily: do not code for reverse transcriptase, transcribed by RNA polymerase III


RETROVIRUSES AS TRANSPOSABLE ELEMENTS: When HIV integrates its genetic sequence into a hosts DNA the Long Terminal Repeat or LTR is a DNA sequence found at the ends of this integrated sequence. ... Retrotransposons are genetic elements that can amplify themselves in a genome and are ubiquitous components of the DNA of many eukaryotic organisms. ... RNA polymerase II (also called RNAP II and Pol II) transcribes DNA to synthesize precursors of mRNA and most snRNA. A 550 kDa complex of 12 subunits, RNAP II is the most studied type of RNA polymerase. ... RNA polymerase III (also called Pol III) transcribes DNA to synthesize ribosomal 5S rRNA, tRNA and other small RNAs. ...

 Retroviruses were first identified as agents involved in the onset of cancer 80years ago.More recently the AIDS epidemic has been shown to be due to the HIV retrovirus.inthe early 1970s it was discovered that retroviruses had the astonishing ability to replicate their RNA genomes via convertion into DNA which became stably integrated in the DNA of the host cell. Itis only comparitivly recently that retroviruses have been rcognized as particularly specialized forms of eukaryotic transposons. In effect they are transposons which move via RNA intermediates that usually can leave the host cells and infect other cells .The integrated DNA form (provirus) of the retrovirus bears a marked similarity to a tronsposon 

The transposition cycle of retroviruses has other similarities to prokaryotic transposons,which suggest a distant familial relationship between this two types of transposon.crucial intermediates in retrovirus transposition are extrachromosomal DNA molecules. These are genrated by copying the RNA of the virus paticle into DNA by a retrovirus -encoded polymerase called reverse transcriptase.the extra chromosomal linear DNA is the direct precursor of the integrated element and the insertion mechanism bears a strong similarity to "cut and paste" transposition.


Class II: DNA transposons

The major difference of Class II transposons from retrotransposons is that their transposition mechanism does not involve an RNA intermediate. Class II transposons usually move by cut and paste, rather than copy and paste, using the transposase enzyme. Different types of transposase work in different ways. Some can bind to any part of the DNA molecule, and the target site can therefore be anywhere, while others bind to specific sequences. Transposase makes a staggered cut at the target site producing sticky ends, cuts out the transposon and ligates it into the target site. A DNA polymerase fills in the resulting gaps from the sticky ends and DNA ligase 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 transposon excision by transposase). In computing, cut and paste is a user-interface paradigm for a means of moving text (typically plain text) or other data from a source to a destination. ... Transposase is an enzyme that binds to single-stranded DNA and can incorporate it into genomic DNA. Class I transposons encode a transposase which allows them to enable transposons to be cut from genomic DNA and be inserted at another location. ... This article or section does not adequately cite its references or sources. ... 3D structure of the DNA-binding helix-hairpin-helix motifs in human DNA polymerase beta A DNA polymerase is an enzyme that assists in DNA replication. ... In molecular biology, DNA ligase is a particular type of ligase (EC 6. ...


Not all DNA transposons transpose through cut and paste mechanism. In some cases a replicative transposition is observed in which transposon replicates itself to a new target site. Replicative transposition is a mechanism of transposition in molecular biology in which the transposable element is duplicated during the reaction, so that the transposing entity is a copy of the original element. ...


The transposons which only move by cut and paste may duplicate themselves if the transposition happens during S phase of the cell cycle when the "donor" site has already been replicated, but the "target" site has not. DNA replication. ... The cell cycle, or cell-division cycle, is the series of events that take place in a eukaryotic cell leading to its replication. ...


Both classes of transposon may lose their ability to synthesise reverse transcriptase or transposase through mutation, yet continue to jump through the genome because other transposons are still producing the necessary enzyme.


Examples

  • The first transposons were discovered in maize (Zea mays), (corn species) by Barbara McClintock in 1948, for which she was awarded a Nobel Prize in 1983. She noticed insertions, deletions, and translocations, caused by these transposons. These changes in the genome could, for example, lead to a change in the color of corn kernels. About 50% of the total genome of maize consists of transposons. The Ac/Ds system McClintock described are class II transposons.
  • One family of transposons in the fruit fly Drosophila melanogaster are called P elements. They seem to have first appeared in the species only in the middle of the twentieth century. Within 50 years, they have spread through every population of the species. Gerald Rubin and Allan Spradling pioneered technology to use artificial P elements to insert genes into Drosophila by injecting the embryo.[2][3][4]
  • Transposons in bacteria usually carry an additional gene for function other than transposition---often for antibiotic resistance. In bacteria, transposons can jump from chromosomal DNA to plasmid DNA and back, allowing for the transfer and permanent addition of genes such as those encoding antibiotic resistance (multi-antibiotic resistant 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 sequences.
  • The most common form of transposon in humans is the Alu sequence. The Alu sequence is approximately 300 bases long and can be found between 300,000 and a million times in the human genome.
  • Mu phage transposition is the best known example of replicative transposition. Its transposition mechanism is somewhat similar to a homologous recombination.

This article is about the maize plant. ... Barbara McClintock (June 16, 1902 – September 2, 1992) was a pioneering American scientist and one of the worlds most distinguished cytogeneticists. ... Year 1948 (MCMXLVIII) was a leap year starting on Thursday (link will display the 1948 calendar) of the Gregorian calendar. ... The Nobel Prize (Swedish: ) was established in Alfred Nobels will in 1895, and it was first awarded in Physics, Chemistry, Physiology or Medicine, Literature, and Peace in 1901. ... Year 1983 (MCMLXXXIII) was a common year starting on Saturday (link displays the 1983 Gregorian calendar). ... An illustration of an insertion at chromosome level Genetic Insertion is the addition of one or more nucleotide base pairs into a genetic sequence. ... A genetic deletion is a genetic aberration in which part of a chromosome is missing. ... Chromosomal translocation of the 4th and 20th chromosome. ... Binomial name Meigen, 1830[1] Drosophila melanogaster (from the Greek for black-bellied dew-lover) is a two-winged insect that belongs to the Diptera, the order of the flies. ... A P element is a transposon that is present in the fruit fly Drosophila melanogaster and is used widely for mutagenesis and the creation of genetically modified flies used for genetics research. ... For other uses, see Species (disambiguation). ... Gerald M. Rubin (born 1950) 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. ... For other uses, see Embryo (disambiguation). ... Phyla/Divisions Actinobacteria Aquificae Bacteroidetes/Chlorobi Chlamydiae/Verrucomicrobia Chloroflexi Chrysiogenetes Cyanobacteria Deferribacteres Deinococcus-Thermus Dictyoglomi Fibrobacteres/Acidobacteria Firmicutes Fusobacteria Gemmatimonadetes Nitrospirae Omnibacteria Planctomycetes Proteobacteria Spirochaetes Thermodesulfobacteria Thermomicrobia Thermotogae Bacteria (singular, bacterium) are a major group of living organisms. ... Antibiotic resistance is the ability of a microorganism to withstand the effects of an antibiotic. ... A scheme of a condensed (metaphase) chromosome. ... Figure 1: Illustration of a bacterium with plasmids enclosed showing chromosomal DNA and plasmids. ... Multidrug resistance is the ability of pathologic cells to withstand chemicals that are designed to aid in the eradication of such cells. ... Insertion sequences (also known as insertion elements, ISs, insertion sequence elements, or IS elements) are short DNA sequences that act as simple transposable elements; insertion sequences only code for transposition enzymes (transposases). ... This article is about modern humans. ... An Alu sequence is a short stretch of DNA originally characterized by the action of the Alu restriction endonuclease. ... An Alu sequence is a short stretch of DNA originally characterized by the action of the Alu restriction endonuclease. ... In biology the genome of an organism is the whole hereditary information of an organism that is encoded in the DNA (or, for some viruses, RNA). ... Bacteriophage or phage Mu is a type of virus that infects bacteria. ... Replicative transposition is a mechanism of transposition in molecular biology in which the transposable element is duplicated during the reaction, so that the transposing entity is a copy of the original element. ... Chromosomal crossover is the process by which two chromosomes, paired up during Prophase I of meiosis, exchange some distal portion of their DNA. Crossover occurs when two chromosomes, normally two homologous instances of the same chromosome, break and then reconnect but to the different end piece. ...

Transposons causing diseases

Transposons are mutagens. They can damage the genome of their host cell in different ways: In biology, a mutagen (Latin, literally origin of change) is a physical or chemical agent that changes the genetic information (usually DNA) of an organism and thus increases the number of mutations above the natural background level. ...

  • A transposon or a retroposon that inserts itself into a functional gene will most likely disable that gene.
  • After a transposon leaves a gene, the resulting gap will probably not be repaired correctly.
  • Multiple copies of the same sequence, such as Alu sequences can hinder precise chromosomal pairing during mitosis, resulting in unequal crossovers, one of the main reasons for chromosome duplication.

Diseases that are often caused by transposons include hemophilia A and B, severe combined immunodeficiency, porphyria, predisposition to cancer, and Duchenne muscular dystrophy. An Alu sequence is a short stretch of DNA originally characterized by the action of the Alu restriction endonuclease. ... A scheme of a condensed (metaphase) chromosome. ... Mitosis divides genetic information during cell division. ... Thomas Hunt Morgans illustration of crossing over (1916) Homologous Recombination is the process by which two chromosomes, paired up during prophase I of meiosis, exchange some distal portion of their DNA. Crossover occurs when two chromosomes, normally two homologous instances of the same chromosome, break and then reconnect but... Haemophilia or hemophilia is the name of any of several hereditary genetic illnesses that impair the bodys ability to control bleeding. ... Severe combined immunodeficiency, or SCID, is a genetic disorder in which both arms (B cells and T cells) of the adaptive immune system are crippled, due to a defect in one of several possible genes. ... Porphyrias are a group of inherited or acquired disorders of certain enzymes in the heme biosynthetic pathway (also called porphyrin pathway). ... Cancer is a class of diseases or disorders characterized by uncontrolled division of cells and the ability of these to spread, either by direct growth into adjacent tissue through invasion, or by implantation into distant sites by metastasis (where cancer cells are transported through the bloodstream or lymphatic system). ... Duchenne muscular dystrophy (DMD) (also known as muscular dystrophy - Duchenne type) is a form of muscular dystrophy that is characterized by decreasing muscle mass and progressive loss of muscle function in male children. ...


Additionally, many transposons contain promoters which drive transcription of their own transposase. These promoters can cause aberrant expression of linked genes, causing disease or mutant phenotypes. A micrograph of ongoing gene transcription of ribosomal RNA illustrating the growing primary transcripts. ... Transposase is an enzyme that binds to single-stranded DNA and can incorporate it into genomic DNA. Class I transposons encode a transposase which allows them to enable transposons to be cut from genomic DNA and be inserted at another location. ... This article is about biological mutants. ... The phenotype of an individual organism is either its total physical appearance and constitution, or a specific manifestation of a trait, such as size or eye color, that varies between individuals. ...


Evolution of transposons

The evolution of transposons and their effect on genome evolution is currently a dynamic field of study.


Transposons are found in all major branches of life. They may or may not 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. While transposons may confer some benefits on their hosts, they are generally considered to be selfish DNA parasites that live within the genome of cellular organisms. In this way, they are similar to viruses. Viruses and transposons also share features in their genome structure and biochemical abilities, leading to speculation that they share a common ancestor. A group of organisms is said to have common descent if they have a common ancestor. ... Horizontal gene transfer (HGT), also Lateral gene transfer (LGT), is any process in which an organism transfers genetic material to another cell that is not its offspring. ... Selfish DNA is DNA which is prevalent in the genome, not because its phenotypic effect is beneficial, but because it has properties which cause the number of copies of it within the genome to increase with time. ... A parasite is an organism that spends a significant portion of its life in or on the living tissue of a host organism and which causes harm to the host without immediately killing it. ... This article is about biological infectious particles. ...


Since excessive transposon activity can destroy a genome, many organisms seem to have developed mechanisms to reduce transposition to a manageable level. Bacteria may undergo high rates of gene deletion as part of a mechanism to remove transposons and viruses from their genomes while eukaryotic organisms may have developed the RNA interference (RNAi) mechanism as a way of reducing transposon activity. In the nematode Caenorhabditis elegans, some genes required for RNAi also reduce transposon activity. Kingdoms Animalia - Animals Fungi Plantae - Plants Chromalveolata Protista Alternative phylogeny Unikonta Opisthokonta Metazoa Choanozoa Eumycota Amoebozoa Bikonta Apusozoa Cabozoa Rhizaria Excavata Corticata Archaeplastida Chromalveolata Animals, plants, fungi, and protists are eukaryotes (IPA: ), organisms whose cells are organized into complex structures by internal membranes and a cytoskeleton. ... Life on Earth redirects here. ... Cells use dicer to trim double stranded RNA to form small interfering RNA or microRNA. An exogenous dsRNA or endogenous pre-miRNA can be processed by dicer and incorporated into the RNA-induced silencing complex (RISC), which targets single-stranded messenger RNA molecules and triggers translational repression;[1] incorporation into... Binomial name Maupas, 1900 Caenorhabditis elegans (IPA: ) is a free-living nematode (roundworm), about 1 mm in length, which lives in temperate soil environments. ...


Transposons may have been co-opted by the vertebrate immune system as a means of producing antibody diversity. The V(D)J recombination system operates by a mechanism similar to that of transposons. The immune system is the collection of organs and tissues involved in the adaptive defense of a body against foreign biological material. ... V(D)J recombination is a mechanism of DNA recombination used by humans and other vertebrates for immunological protection against attacks by bacterial, viral, and parasitic invaders. ...


Evidence exists that transposable elements may act as mutators in bacteria.


Applications

Transposons were first discovered in the plant maize (Zea mays, corn species), which is named dissociator (Ds). Likewise, the first transposon to be molecularly isolated was from a plant (Snapdragon). Appropriately, transposons have been an especially useful tool in plant molecular biology. Researchers use transposons as a means of mutagenesis. In this context, a transposon jumps into a gene and produces a mutation. The presence of the transposon provides a straightforward means of identifying the mutant allele, relative to chemical mutagenesis methods. This article is about the maize plant. ... Species This list is currently incomplete Section Antirrhinum Antirrhinum australe Antirrhinum barrelieri Antirrhinum boissieri Antirrhinum braun-blanquetii Antirrhinum charidemi Antirrhinum graniticum Antirrhinum grosii Antirrhinum hispanicum Antirrhinum latifolium Antirrhinum lopesianum Antirrhinum majus Antirrhinum meonanthum Antirrhinum microphyllum Antirrhinum molle Antirrhinum onubensis Antirrhinum pertegasii Antirrhinum pulverulentum Antirrhinum rupestre Antirrhinum sempervirens Antirrhinum siculum Antirrhinum...


Sometimes the insertion of a transposon into a gene can disrupt that gene's function in a reversible manner; transposase mediated excision of the transposon restores gene function. This produces plants in which neighboring cells have different genotypes. 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. This article does not cite any references or sources. ...


Transposons are also a widely used tool for mutagenesis of all experimentally tractable organisms.


See also

Insertion sequences (also known as insertion elements, ISs, insertion sequence elements, or IS elements) are short DNA sequences that act as simple transposable elements; insertion sequences only code for transposition enzymes (transposases). ... The selfish gene theory postulates that natural selection will increase the frequency of those genes whose phenotypic effects ensure their successful replication. ... Tn 10 is a transposable element; a sequence of DNA that is capable of mediating its own movement through the DNA of host organisms. ... Often abbreviated to STM, Signature-Tagged Mutagenesis is a genetic technique used to study gene function. ...

References

  • Quesneville H; Bergman CM, Andrieu O; Autard D; Nouaud D; et al. (2005). "Combined evidence annotation of transposable elements in genome sequences". PLoS Comp Biol 1 (2): e22. doi:10.1371/journal.pcbi.0010022. PMID 16110336. 
  • Kidwell, M.G. (2005). "Transposable elements.", in (ed. T.R. Gregory): The Evolution of the Genome. San Diego: Elsevier, 165-221. ISBN 0-12-301463-8. 
  • Craig NL, Craigie R, Gellert M, and Lambowitz AM (ed.) (2002). Mobile DNA II. Washington, DC: ASM Press. ISBN 978-1555812096. 
  • Lewin B (2000). Genes VII. Oxford University Press.. ISBN 978-0198792765. 

A digital object identifier (or DOI) is a standard for persistently identifying a piece of intellectual property on a digital network and associating it with related data, the metadata, in a structured extensible way. ... // Summary The Evolution of the Genome is a book edited by Dr. T. Ryan Gregory of the University of Guelph, Ontario, Canada, covering a wide range of topics in the study of genome evolution. ...

Notes

  1. ^ McCLINTOCK, B. (Jun 1950). "The origin and behavior of mutable loci in maize.". Proc Natl Acad Sci U S A. 36 (6): 344-55. PMID 15430309. 
  2. ^ Spradling AC, Rubin GM. Transposition of cloned P elements into Drosophila germ line chromosomes. Science. 1982 Oct 22;218(4570):341–347.
  3. ^ Rubin, G.M., Spradling, A.C. (1982). Genetic transformation of Drosophila with transposable element vectors. Science 218(4570): 348-353.
  4. ^ Francesca Cesari, "Milestones in Nature: Milestone 9: Transformers, Elements in Disguise", Nature, Oct. 15, 2007.

External links

  • Kimball's Biology Pages: Transposons
  • A possible connection between aberrant reinsertions and lymphoma - New Scientist
  • Precision genetic engineering Inserting new genes into plant cells - new gene transfer methods
  • Wiki specially dedicated to the transposable elements

  Results from FactBites:
 
Transposon - definition of Transposon in Encyclopedia (972 words)
Transposons are sequences of DNA that can move around to different positions within the genome of a single cell, a process called Transposition.In the process, they can cause mutations, and change the amount of DNA in the genome.
Transposons can move directly from one position to another within the genome, while retrotransposons have first to be transcribed to RNA and then back to DNA by reverse transcriptase.
Transposons are also a widely used tool for mutagenesis in Drosophila melanogaster, and in a wide variety of bacteria to study gene function.
Transposon - Wikipedia, the free encyclopedia (1247 words)
Transposons are sequences of DNA that can move around to different positions within the genome of a single cell, a process called transposition.
Both classes of transposon may lose their ability to synthesise reverse transcriptase or transposase through mutation, yet continue to jump through the genome because other transposons are still producing the necessary enzyme.
While transposons may confer some benefits on their hosts, they are generally considered to be selfish DNA parasites that live within the genome of cellular organisms.
  More results at FactBites »

 
 

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