Transposon

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A transposon (colloquially jumping gene ) is a DNA section of certain length in the genome , which can change its position in the genome (transposition). A distinction is made between transposons whose mobile intermediate stage is formed by RNA ( retroelements or class I transposon) and those whose mobile phase is DNA (DNA transposon or class II transposon). In contrast to the retro element, transposons can change their locus without an intermediate RNA stage. Transposons are known as a form of selfish DNA , although they can be of benefit to their host .

properties

When transposons are autonomous, that is, they bring their own “tools for jumping” with them, they are often surrounded by short repetition sequences (repeats) that are necessary for the transposition. The orientation of these repetition sequences can be in the same direction (direct repeat) or in opposite directions (inverted repeat) . The typical nature of the repeat sequences is often used to classify transposons. Complete, autonomous transposons contain one or more genes; one of the genes always codes for a transposase .

Transposons are bounded by a small (8–40 bp ), reverse-identical, non-informative nucleotide sequence ( inverted repeat or IR); these are essential for the functioning of the transposase (the enzyme responsible for jumping ). Furthermore, DNA transposons are also surrounded by 3–13 bp long direct repeats . However, these belong to the host DNA and arise from the fact that when integrating, similar to a restriction enzyme , the two strands are cut in an offset manner, then the transposon is integrated and the single strands are replenished by the cell's own repair enzymes . These direct repeats are therefore also referred to as target site duplications . When cutting out these duplications often remain so "Footprints" ( footprints ) remain the excision of DNA transposons, one insertion represent. In some cases, both duplications are cut out so that a deletion effectively occurs (the duplications are from the host DNA).

Discovery and Importance

The transposons were discovered in corn in 1948 by the American botanist Barbara McClintock , who was honored with the Nobel Prize in 1983 for this discovery . Since then, transposons have also been found in many other organisms, including humans . In genetics and developmental biology especially the transposons of play Drosophila melanogaster a major role, since they can be selectively injected into the flies and stably integrated into the genome. In this way, genetically modified transposons make it relatively easy to produce transgenic flies that play an important role in researching gene functions. However, transposons can also be transferred to plasmids or phage genomes , which can lead to infectious mutations . The newly inserted genetic information can make bacteria resistant to antibiotics .

Transposons make up about 3% of the human genome, common families are MER-1 (approx. 1.4%) and MER-2 (approx. 1.0%). A well-supported theory assumes that the recombinases RAG1 and RAG2, which are responsible for V (D) J recombination in immunoglobulin production, are derived from transposases, which means that the vertebrate immune system is derived from DNA transposons.

DNA transposons can also jump onto plasmids and thus contain resistance genes through the cointegrates . It cannot therefore be ruled out that they play a role in the spread of resistance to antibiotics . Around 45% of the human genome consists of transposable elements, but only a very small proportion of them are capable of jumping. There is also the theory that the immunoglobulins are derived from transposons. In this respect it is debatable whether one should count transposons as junk DNA . Research by Eric Lander et al. (2007) show, however, that transposons have a very important function, since as a creative factor in the genome they can quickly spread important genetic innovations in the genome.

Other organisms have a different genome proportion of transposons, for example only about 15–22 % of the genome in D. melanogaster and about 12% of the genome in Caenorhabditis elegans . In some plants such as B. maize, however, over 80% of the genome can be transposons. The following table gives an overview of the proportions of transposable elements in genomic DNA.

Genome size and proportion of transposable elements
species Genome mass
in picograms 		Genome size
in giga base pairs 		Percentage of
transposable elements
Rana esculenta frog 5.6-8.0 5.5-7.8 77
Zea mays Corn 5.0 4.9 85
homo sapiens human 3.5 3.4 45
Mus musculus mouse 3.4 3.3 40
Drosophila melanogaster Fruit fly 0.18 0.17 15-22
Caenorhabditis elegans worm 0.1 0.098 12
Saccharomyces cerevisiae yeast 0.012 0.0117 3-5
Escherichia coli bacterium 0.0046 0.0045 0.3

Propagation Mechanisms

In the case of DNA transposons, a distinction is made between conservative transposition and replicative transposition . While with conservative transposition the transposon is cut out of the DNA and inserted again in another place ("Cut & Paste"), with the replicative transposon the transposon is not cut out, but a copy is made which is inserted in another place ("Copy & Paste "). With replicative transposition, the number of transposons is increased. The transposon is cut out or copied with the aid of the enzyme transposase .

DNA transposons that are too small to encode a protein are known as miniature inverted-repeat transposable elements (MITEs). They cannot spread autonomously. How they reproduce or shift is still unclear. The transposase gene may have been present once and is now defective or lost. MITEs may be copied and shifted by transposase enzymes which are encoded by other, larger transposons and have the same recognition sequence (inverted repeats).

RNA transposons, or better: retro elements jump by being transcribed into mRNA , which are then transcribed into cDNA (by a reverse transcriptase ) and reintegrated. The retro elements multiply. The subclass of the so-called SINEs , but also other retro elements that are no longer autonomous, no longer have a reverse transcriptase and are dependent on a foreign one (e.g. from other retro elements).

Functional classification of transposable elements

Depending on whether the intermediate element is DNA or RNA , a distinction is made between DNA transposons (also called class II transposons) and so-called retro elements (class I transposons). The retro elements either have long terminal repeats (LTR; with LTR retrotransposons or retrotransposons in the narrower sense and with classic retroviruses ) or not ( retroposons ).

Evolution of the transposons

The evolution of transposons and their effects on the evolution of the genome is currently the subject of controversial research.

Transposons are found in all branches of life. However, it is unknown whether they were inherited from the “ primal ancestor ”, or whether they arose several times independently of one another, or possibly emerged once and then spread among living beings through horizontal gene transfer . A study published in 2008 gives strong indications for the latter. Almost identical sp ace- in- vader (SPIN) genes are found in species as different as mice and frogs. Although transposons can provide benefits to their host, they are generally regarded as selfish DNA - parasites classified which cellular genomes in organisms "live". In this way they are similar to viruses . Viruses and transposons have similarities in their genome structure and their biochemical properties. This leads to the speculation that viruses and transposons could have a common ancestor (see Nucleocytoviricota § External Systematics ).

Interestingly, transposons often encode the enzyme transposase , which plays an important role in the replication mechanism of the transposon itself. This could be interpreted as a virus-like property, since the genetic material of viruses also encodes precisely the gene products that serve to spread this virus genome.

Since excessive transposon activity can destroy the genome, many organisms seem to have developed mechanisms that reduce transposition to a manageable level. Bacteria can have a high rate of gene deletion as part of a mechanism designed to remove transposons and viruses from their genome. In contrast, eukaryotic organisms may have developed the RNA interference (RNAi) mechanism to restrict transposon activity. In the nematode Caenorhabditis elegans , some genes required for RNAi reduce transposon activity.

Phase variation

In certain strains of Salmonella typhimurium , a transposon is responsible for ensuring that the organism switches between two variations of flagellin , the main component of the flagellum , approximately every 1000 generations . Since both variants are recognized by different antibodies, this is beneficial for the organism.

Groups of prokaryotic transposons

The only gene that is contained in an insertion sequence encodes the enzyme transposase . This catalyzes the movement of the transposon from one place in the DNA to another. This is mostly a conservative transposition. Only rarely is it transposed in a replicative manner (old sequence is retained). The transposase gene is flanked on both sides by inverted repeats .

In addition to the transposase, the so-called Tn3 family also has a resolvase (tnpR) and contains a so-called res site. In contrast to those of the IS elements, transposases of the Tn3 family do not necessarily cut at their own IR, but also at more distant IR This includes a large piece of host DNA (cointegrate), which is cut out by the resolvase in the res site. The Tn3 family also transposes preferentially replicatively.

Some phages , such as the phage Mu, also belong to the DNA-transposable elements. The phages multiply in the provirus stage, i.e. integrated in the genome through transposition.

Eukaryotic transposons

Eukaryotic transposons are only partially similar to the prokaryotic representatives. In particular, the transposition mechanisms are quite different and some DNA transposons also have an intron - exon structure.

The Ac element is well known , on which Barbara McClintock postulated "jumping" elements in corn in 1951 and for which she received a Nobel Prize in 1983 .

In Drosophila melanogaster , the p elements are known representatives of DNA transposons.

Trivia

A synthetic transposon ( Sleeping Beauty ) has been named "Molecule of the Year 2009" by the International Society for Molecular and Cell Biology and Biotechnology Protocols and Researches (ISMCBBPR) .

See also

literature

Web links

Individual evidence

  1. ↑ Eric Lander et al. a .: Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. In: Nature. Volume 447, May 10, 2007, pp. 167-177.
  2. ↑ Patrick S. Schnable, Doreen Ware, Robert S. Fulton, Joshua C. Stein, Fusheng Wei: The B73 Maize Genome: Complexity, Diversity, and Dynamics . In: Science . tape 326 , no. 5956 , November 20, 2009, ISSN  0036-8075 , p. 1112–1115 , doi : 10.1126 / science.1178534 , PMID 19965430 ( sciencemag.org [accessed April 12, 2018]).
  3. ↑ Christian Biémont, Cristina Vieira: Junk DNA as force of evolutionary . In: Nature . Vol. 443, pp. 521-524, PMID 17024082 .
  4. ↑ Converted from Biemont et al. with a conversion factor of 0.978 · Gigabase pairs per picogram.
  5. ↑ Miniature Inverted-Repeat Transposable Elements (MITEs) ( Memento of the original dated February 6, 2006 in the Internet Archive ) Info: The archive link was inserted automatically and has not yet been checked. Please check the original and archive link according to the instructions and then remove this notice. ; Kimball's Biology Pages, December 5, 2011. @1@ 2Template: Webachiv / IABot / users.rcn.com
  6. ↑ John K. Pace II, Clément Gilbert, Marlena S. Clark, Cédric Feschotte1: Repeated horizontal transfer of a DNA transposon in mammals and other tetrapods. On: pnas.org ; published in: Proceedings of the National Academy of Sciences . (PNAS), Volume 105, No. 44 of November 4, 2008, pp. 17023-17028 (English).
  7. ↑ Guenther Witzany: Natural Genome Editing Competences of Viruses. In: Acta Biotheor. Volume 54, 2006, pp. 35-253.
  8. ^ Donald Voet, Judith Voet: Biochemistry. 2nd edition, Wiley & Sons, 1995, ISBN 0-471-58651-X , p. 1059.
  9. ↑ Barbara Bachtler (Science Information Service): “Sleeping Beauty” is molecule of the year. Press release from January 19, 2010.
  10. ↑ Wayne W. Grody: ISMCBBPR's President Isidro AT Savillo announces the Molecule of the Year 2009 as Sleeping Beauty Transposase SB 100X. (English).