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Mobile DNA

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Mobile DNA consists of blocks of DNA that are able to move and insert into new locations throughout the genome without needing DNA sequence similarity or requiring the process of homologous recombination to enable movement.

Such a process of movement and insertion is often called transposition, and the mobile DNAs are frequently called transposons. Some mobile DNAs ('DNA elements') such as retrotransposons move by different mechanisms than used by strictly defined transposons, but achieve the same overall outcome - namely movement of blocks of DNA to new positions in chromosomes.

The general topic of mobile DNA also encompasses other genetic entities that are able to move between organisms such as plasmids and viruses, which in some situations reside within cells permanently as an extra, optional, replicating chromosome. Plasmids and bacterial viruses (bacteriophages) are involved in much movement of mobile DNA between different microorganisms, and plasmids often carry a variety of different transposons.

Contents

Transposition

Transposition is a process where sections of DNA move throughout the genome, often making copies of themselves at the same time. Not all DNA does this, only sections called transposons, transposable elements, or jumping genes.

Transposons have been called junk DNA, because they have no known useful function, and selfish DNA because they exploit the genetic mechanisms of the cell. A more modern view is that these terms do not accurately convey the full range of transposon behavior, which ranges from parasitism to mutualism.

Their activities have conferred upon pathogenic bacteria the disturbing advantage of acquiring resistance to a number of antibiotics, and then transmitting this multiple drug resistance in a highly infectious way.

Increasingly transposons are being seen to participate in evolution of new function and complex regulatory circuits in multicellular organisms [1][2]. (See Effects of transposons on the genome.)

The mechanism of transposition

Transposons usually code for at least one gene, as they need the enzyme transposase, and the transposon usually codes for this itself. The ends of the transposon consist of terminal DNA repeats which the transposase binds to. The transposase also binds to the target site on the genome, which is cut to leave "sticky ends', or single stranded DNA overhangs similar to those created by restriction endonucleasess. Depending on the type of transposon it is then either copied or cut out and inserted into the target site by the action of the enzyme DNA ligase. Some transposons encode mechanisms for copying themselves, but many exploit the cell's own DNA copying mechanisms.

For more on the mechanisms see Types of transposon.

Types of transposon

There are three different types of transposon, classified by their mechanisms:

Class I: retrotransposons

See main article Retrotransposon

Retrotransposons (sometimes Retroposons) work by copying themselves and pasting copies back into the genome, in multiple places. First retrotransposons copy themselves to RNA (transcription), but instead of being translated the RNA is picked up by reverse transcriptase (often coded by the transposon itself) which copies the RNA back into DNA which is then inserted into the genome. This process is called retroposition, and the new genes are called retrogenes. Retrotransposons usually have very long terminal repeats of over 1000 base pairs, making them easy to find and study.

Retrotransposons behave very similarly to retroviruses, such as HIV, giving a clue to their evolutionary origins (see #The evolution of transposons).

Retrotransposons can carry flanking sequence during their mobilization to a new site, a process which is called 3'-transduction, and which can cause duplication of genes. Such gene duplication is an important mechanisms for creating new genes and generating genomic novelty.

The duplication of entire genes and the creation of previously undescribed gene families through retrotransposon-mediated flanking DNA sequence transduction has been highlighted recently as an important mechanism by which mobile DNA impacts the host genome during evolution[3].

Class II transposons

Class II transposons 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. The transposase then cuts the target site to produce sticky ends, cuts out the transposon and ligases it into the target site, and then fills in the sticky ends with their base pairs.

Transposons may lose their ability to synthesize transposase through mutation, yet continue to jump through the genome because other transposons are still producing transposase. It is possible that some transposons become transposons simply by mutations producing the sequences that signals to transposase.

P elements

P elements are a particular type of class II transposon that was first detected in Drosophila (fruit flies) in the 1950s. P elements are so good at spreading that they cause so many mutations in the germ line cells as to sterilize the flies. Drosophila have evolved a mechanism for suppressing transposase, however, and all except a few isolated lab populations are immune to the effects of P elements. The roundworm Caenorhabditis elegans has evolved an RNA interference system to respond to a similar problem of transposons.

MULEs and PACK-MULES

The Mutator (Mu) transposons of maize are known to capture pieces of host genes and then rapidly amplify them via subsequent duplications. [4]. Related Mu Like Elements (MULEs) are a widely distributed plant and fungal transposon family that are thought to be the result of this process. [5] [6] [7]

Similar examples of gene capture have been observed in other class II elements such as CACTA elements[8], hAT elements[9], and Helitrons,[10], suggesting that this gene capture process may be a feature of many transposons. [11]

MULEs have terminal inverted repeats (TIRs) [12] [13], and the inverted repeats (TIRs) from MULEs often flank the captured fragments of host genes. Such TIRs of MULEs with captured genes are referred to as Pack-MULEs.

There are over 3,000 Pack-MULEs in rice containing fragments derived from more than 1,000 cellular genes. Pack-MULEs frequently contain fragments from multiple genes that are fused to form new genes. Some captured gene fragments in rice PACK-MULES may be functional new genes. [14]

Class III: Miniature Inverted-repeat transposable elements

MITEs are sequences of about 400 base pairs and 15 base pair inverted repeats that vary very little. They are found in their thousands in the genomes of both plants and animals (over 100,000 were found in the rice genome). MITEs are too small to encode any proteins.

Effects of transposons on the genome

Transposons can cause mutation. They do this either by being inserted into the coding region of a gene, losing some of the gene in the process, or by being inserted upstream of the coding region of a gene in an area important in determining the expression of the gene, such an area where a transcription factor would bind to the DNA. Insertion into a gene can also cause alternative splicing leading to a greater diversity of proteins produced by a single gene.

Both transposons and retrotransposons can cause segments of DNA to be duplicated, an important first stage in the Evolution of new information, and a process that lead more rapid sequence change in the duplicated genes which are less constrained by purifying selection.

Retrotransposons have been shown to be active in promoting much gene evolution in primate genomes, including the human genome - by creating new genes and generating genomic novelty.

For instance, SVA is the youngest retrotransposon family in primates is able to capture 3' flanking sequences during retrotransposition (that is carry out 3'-transduction to effectively duplicate genes).

Recent study of the human genome the human genome has shown that about 53 thousand base-pairs of genomic sequences have been duplicated by 143 different SVA-mediated flanking gene capture (3' transduction) events.

One group of SVA elements that duplicated the entire AMAC gene three times in the human genome which happened before the divergence of humans and African great apes. In addition to the original AMAC gene, the three transduced (duplicated) AMAC copies contain intact protein coding sequences in the human genome, and at least two are actively transcribed in different human tissues..[15]

Transposons are involved the creation of new "chimeric" (hybrid) proteins by gene fusion , and in generation of the circuitry of complex new gene regulatory networks during natural evolution.

An important illustration of this evolutionary role has been found in human evolution, involving a member of the mariner-family transposons called Hsmar1. Hsmar1 (Homo sapiens mariner) is present in the human genome as around 1500 copies of mobile DNA.

SETMAR, a new primate chimeric gene resulting from fusion of a SET histone methyltransferase gene to the transposase gene of Hsmar1 mobile DNA The transposase gene was recruited as part of SETMAR 40-58 million years ago in an anthropoid ape, after the insertion of an Hsmar1 transposon downstream of a preexisting SET gene. [16]

Transposition of genes to new chromosomal locations via retrotransposons (retroposition) has generated a significant number of new functional genes (retrogenes) in mammalian and invertebrate animal genomes. A burst of retroposition in primates led to emergence of many new human genes during primate evolution over the last ~63 million years of primate evolution. [17] [18] [19] .

Transposons also increase the size of the genome, because they leave multiple copies of themselves in the genome. For instance, the maize genome has doubled in size in the past 3–6 million years, largely due to a massive burst of retrogene formation. [20]

Transposons can play a part in causing diseases including cancer and haemophilias A (when the Factor VIII gene is disrupted) and B (Factor IX.

The evolution of transposons

The evolution of transposons is an area of much current research, and we can't yet say exactly how transposons came about. However, we do know that many similar transposons can be found in all major groups of organisms on earth. There are three plausible hypotheses as to how this came about:

The hypothesis that transposons can be spread in viruses is supported by evidence in bacteria. In many bacteria transposons contain genes for antibiotic resistance, and when snipped out of the bacteria's circular DNA the plasmids produced can be transferred to other bacterial cells, spreading the resistance to other species by horizontal gene transfer.

In terms of gene selection, there is an obvious selective advantage for bits of DNA that do nothing but copy themselves and allow the rest of the genome to do all the hard work, from the point of view of that piece DNA. At first sight it would like like transposons are bad for the genone as a whole, jumping around causing mutations and silencing of genes, and that organisms would evolve defenses against these DNA parasites. It's possible, however, that transposons are actually selectively advantageous for the genome as a whole. The bulking out of the genome with transposons and other non-coding DNA could make gene regulation easier. Some retrotransposons and retroviruses have sequences similar to the exon, promoter and enhancer regions and DNA, and this may also play a part in gene regulation, or provide a good evolutionary substrate. Transposon activity is greater when the organism is under stress, and this could lead to increased mutation rates when an organism is in an environment it is not well adapted to. There is also evidence that genomes are more stable and better able to survive temperature stress the larger they are.

The discovery of transposons

Transposons were first discovered in maize in 1948 by Barbara McClintock[21]. McClintock noticed unusual genetic behavior such as maize kernel variegation and genetic instability that she attributed to DNA insertion, deletion translocation, and somatic mutation events. Such observation were not new to science. [22] but McClintock's interpretation of it was "before it's time". Her discovery of mobile DNA was initially greeted with widespread skepticism as the interpretation of the strange behavior did not fit with conventional genetics ideas of that time of that time. However, as more evidence for mobile DNA in microorganisms, plant and insects became known ,the significance of her discovery was widely recognized (See Barbara McClintock). In 1983 McClintock was awarded the Nobel Price in Physiology or Medicine.

Some uses for transposons

For more information, see: Transposons as a genetic tool.

Transposons can be exploited by scientists for studying genetics. Because transposons insert themselves into genes they can be used to knock out genes. This technique turns genes off so that their function can be determined, and has been experimentally exploited in microorganisms, plants and animals [23][24].

Plasmids and horizontal movement of mobile DNA between species

See Plasmids, Horizontal gene transfer in prokaryotes

References

Citations

  1. Kidwell MG, Lisch DR.(2001) Perspective: transposable elements, parasitic DNA, and genome evolution. Evolution Int J Org Evolution. 2001 Jan;55(1):1-24.
  2. Bowen NJ Jordan IK (2002) Transposable elements and the evolution of eukaryotic complexity Curr Issues Mol Biol. 2002 Jul;4(3):65-76.
  3. Xing J, Wang H, Belancio VP, Cordaux R, Deininger PL, Batzer MA. (2006) Emergence of primate genes by retrotransposon-mediated sequence transduction. Proc Natl Acad Sci U S A. 2006 Nov 21;103(47):17608-13. Epub 2006 Nov 13.
  4. Talbert LE, Chandler VL. 1988. Characterization of a Highly Conserved Sequence Related to Mutator Transposable Elements in Maize. Molecular Biology and Evolution 5:519–529. PMID 2848175
  5. Yu ZH, Wright SI, Bureau TE. 2000. Mutator-like elements in Arabidopsis thaliana: Structure, diversity and evolution. Genetics 156:2019– 2031. PMID 11102392
  6. Mao L, Wood TC, Yu YS, Budiman MA, Tomkins J, et al. 2000. Rice transposable elements: A survey of 73,000 sequence-tagged-connectors. Genome Research 10:982–990.
  7. Lisch D. 2002. Mutator transposons. Trends in Plant Science 7:498–504. PMID 12417150
  8. Kawasaki S, Nitasaka E. 2004. Characterization of Tpn1 family in the Japanese morning glory: En/Spm-related transposable elements capturing host genes. Plant and Cell Physiology 45:933–944. PMID 15295077
  9. Rubin E, Levy AA. 1997. Abortive gap repair: Underlying mechanism for Ds element formation. Molecular and Cellular Biology 17:6294–6302. PMID 9343390
  10. Lal SK, Giroux MJ, Brendel V, Vallejos CE, Hannah LC. 2003. The maize genome contains a Helitron insertion. Plant Cell 15:381–391. PMID 12566579
  11. Lisch, D. (2005) Pack-MULEs: theft on a massive scale. Bio-Essays 27:353–355 PMID 15770680
  12. Talbert, L. E. & Chandler, V. L. (1988) Characterization of a highly conserved sequence related to mutator transposable elements in maize. Mol. Biol. Evol. 5, 519–529 PMID 2848175
  13. Bennetzen, J. L.& Springer, P. S. (1994) The generation of mutator transposable element subfamilies in maize. Theor. Appl. Genet. 87, 657–667
  14. Jiang N, Bao ZR, Zhang XY, Eddy SR, Wessler SR. (2004) Pack-MULE transposable elements mediate gene evolution in plants. Nature, 431: 569–573 PMID 15457261
  15. Xing J, Wang H, Belancio VP, Cordaux R, Deininger PL, Batzer MA. (2006) Emergence of primate genes by retrotransposon-mediated sequence transduction. Proc Natl Acad Sci U S A. 2006 Nov 21;103(47):17608-13. Epub 2006 Nov 13.
  16. Cordaux R, Udit S, Batzer MA, Feschotte C. (2006) Birth of a chimeric primate gene by capture of the transposase gene from a mobile element. Proc Natl Acad Sci U S A. 2006 May 23;103(21):7941-2.
  17. Marques AC, Dupanloup I, Vinckenbosch N, Reymond A, Kaessmann H (2005) Emergence of Young Human Genes after a Burst of Retroposition in Primates. PLoS Biol 3(11): e357 DOI: 10.1371/journal.pbio.0030357
  18. Long M, Betran E, Thornton K, Wang W (2003) The origin of new genes: Glimpses from the young and old. Nat Rev Genet 4:865–875. PMID 14634634
  19. Emerson JJ, Kaessmann H, Betran E, Long M (2004) Extensive gene traffic on the mammalian X chromosome. Science 303:537–540. PMID 14739461
  20. SanMiguel P, Gaut BS, Tikhonov A, Nakajima Y, Bennetzen JL. (1998) The paleontology of intergene retrotransposons of maize. Nature Genetics 20:43–45. PMID 9731528
  21. Fedoroff, Nina.(2004) The discovery of transposition. James and Bartlett Virtual Text, Great Experiments. Last Revised on October 20, 2004
  22. de Vries, H. (1905). Species and varieties: their origin by mutation (Chicago: Open Court Publishing Co.). Emerson, R. A. (1917). Genetical studies of variegated pericarp in maize. Genetics 2, 1-35. Emerson, R. A. (1929). The frequency of somatic mutation in variegated pericarp of maize. Genetics 14, 488-511. Emerson, R. A. (1914). The inheritance of a recurring somatic variation in variegated ears of maize. Am. Nat. 48, 87-115. Rhoades, M. M. (1938). Effect of the Dt gene on the mutability of the a1 allele in maize. Genetics 23, 377-397. Rhoades, M. M. (1941). The genetic control of mutability in maize. Cold Spring Harbor Symp. Quant. Biol. 9, 138-144. Rhoades, M. M. (1945). On the genetic control of mutability in maize. Proc. Natl. Acad. Sci. USA 31, 91-95.
  23. Kleckner, N. J. Roth, J. and Botstein, D. (1977) Genetic engineering in vivo using translocatable drug-resistance elements. J. Molecular Biology, 116, pages 125-159
  24. Enhancer and Gene Trap Transposon Mutagenesis in Arabidopsis A comprehensive article on the use of Ac/Ds and other transposons for plant mutagenesis

Further reading

See also

The following are similar to transposons in their overall consequences for evolution:

This page was originally derived December 5 2006 from Transposition, part of the EvoWiki encyclopedia of genetics and molecular biology. Further use is subject to the Creative Commons Licence conditions.

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