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Transposon Excision
Transposon Excision DB Haniford, University of Western Ontario, London, ON, Canada
© 2001 Elsevier Inc. All rights reserved.
This article is reproduced from the previous edition, volume 4, p 1966, © 2001, Elsevier Inc.
Transposons are mobile genetic elements. Their movement within and between DNA molecules can result in a wide range of genome rearrangements including insertions, dele tions, inversions, duplications, replicon fusions, and probably chromosomal translocations. In addition, they are important elements in the spread of antibiotic resistance genes in bacteria. They are extremely abundant, being found in almost all organ isms. They can constitute a significant percentage of the total genomic DNA of a species. A large number of different types of transposons have been identified. Of these, a fairly large subset transpose by a mechan ism in which the transposon is simply excised from the flanking ‘donor’ DNA by a pair of double-strand breaks, one at each transposon end. The excised transposon intermediate is then inserted into a new site. The new location usually has no sequence relationship to the transposon or the donor site. Excision and insertion steps are catalyzed by one or more transposon-encoded proteins called transposases. Three different strategies for generating the excised transposon intermediate have been documented. Two separate transposase proteins can be involved in making the double-strand break at each end. For example, in Tn7 (a bacterial transposon), the proteins TnsB and TnsA each are responsible for cleaving a differ ent DNA strand at and just outside of the transposon end, respectively. However, other transposons such as the bacterial transpo sons Tn10 and Tn5 encode only a single transposase protein with a single active site. The excision reaction takes place within a nucleoprotein complex in which there are only two molecules of the transposase present. In this situation, excision takes place by a mechanism in which a transposon end hairpin intermedi ate is formed. Here, the single active site of one transposase monomer first introduces a nick to expose a 3′-OH group at the transposon terminus. Then the same active site is used to catalyze the joining of this 3′-OH terminus to a phosphate group on the opposite strand of the same end. This generates the transposon end hairpin and severs the final connection between the transposon and the flanking donor DNA in one chemical step. The hairpin end must then be cleaved to reex pose the 3′-OH group for joining to the target DNA in the final step. It is likely that a number of plant transposons also use this mechanism of excision. In the third excision mechanism, the transposase first makes a nick at only one transposon end. Then the exposed 3′-OH terminus is joined to a phosphate group on the same
Brenner’s Encyclopedia of Genetics, 2nd edition, Volume 7
DNA strand but just outside of the second end. This generates an excision intermediate in which the cleaved strand forms a covalently closed circle and the two transposon ends are held together by a single-strand bridge. Double-strand circles are generated from this by an as yet undefined mechanism. Then the transposase introduces a pair of single-strand cleavages at the abutting transposon ends. This opens up the circle gener ating a linear form of the excised transposon that can be directly inserted into a new target site. This mechanism is used by the bacterial transposon IS911 and other members of the IS3 family. It is not understood what constraints are responsible for the evolution of this seemingly complex exci sion pathway. Interestingly, the hairpin mechanism for transposon exci sion is also used in the formation of double-strand DNA breaks in V(D)J recombination. This is the process whereby antigen receptor genes are pieced together from separate coding seg ments in developing T and B cells in the immune systems of jawed vertebrates. Furthermore, the proteins that catalyze this double-strand break reaction, RAG1 and RAG2, have been shown to catalyze DNA transposition reactions in vitro via the hairpin mechanism. The use of a common mechanism for double-strand break formation in V(D)J recombination and bacterial DNA transposition suggests that the V(D)J recombi nation system evolved from an ancient bacterial transposon. It will be interesting to see if other mechanisms for carrying out transposon excision are used and what constraints favor these mechanisms.
See also: Insertion Sequences; Transposable Elements.
Further Reading Kennedy AK, Guhathakurta A, Kleckner N, and Haniford DB (1998) Tn10 transposition via a DNA hairpin intermediate. Cell 95: 125–134. McBlane JF, van Gent DC, Ramsden DA, et al. (1995) Cleavage at a V(D)J recombination signal requires only RAG1 and RAG2 proteins and occurs in two steps. Cell 83: 387–395. Sarnovsky RJ, May EW, and Craig NL (1996) The Tn7 transposase is a heteromeric complex in which DNA breakage and joining activities are distributed between different gene products. The EMBO Journal 15: 6348–6361. Ton-Hoang B, Betermier M, Polard P, and Chandler M (1997) Assembly of a strong promoter following IS911 circularization and the role of circles in transposition. The EMBO Journal 16: 3357–3371. Turlan C and Chandler M (2000) Playing second fiddle: Second-strand processing and liberation of transposable elements from donor DNA. Trends in Microbiology 8: 268–274.
doi:10.1016/B978-0-12-374984-0.01572-2
165
© 2001 Elsevier Inc. All rights reserved.
This article is reproduced from the previous edition, volume 4, p 1966, © 2001, Elsevier Inc.
Transposons are mobile genetic elements. Their movement within and between DNA molecules can result in a wide range of genome rearrangements including insertions, dele tions, inversions, duplications, replicon fusions, and probably chromosomal translocations. In addition, they are important elements in the spread of antibiotic resistance genes in bacteria. They are extremely abundant, being found in almost all organ isms. They can constitute a significant percentage of the total genomic DNA of a species. A large number of different types of transposons have been identified. Of these, a fairly large subset transpose by a mechan ism in which the transposon is simply excised from the flanking ‘donor’ DNA by a pair of double-strand breaks, one at each transposon end. The excised transposon intermediate is then inserted into a new site. The new location usually has no sequence relationship to the transposon or the donor site. Excision and insertion steps are catalyzed by one or more transposon-encoded proteins called transposases. Three different strategies for generating the excised transposon intermediate have been documented. Two separate transposase proteins can be involved in making the double-strand break at each end. For example, in Tn7 (a bacterial transposon), the proteins TnsB and TnsA each are responsible for cleaving a differ ent DNA strand at and just outside of the transposon end, respectively. However, other transposons such as the bacterial transpo sons Tn10 and Tn5 encode only a single transposase protein with a single active site. The excision reaction takes place within a nucleoprotein complex in which there are only two molecules of the transposase present. In this situation, excision takes place by a mechanism in which a transposon end hairpin intermedi ate is formed. Here, the single active site of one transposase monomer first introduces a nick to expose a 3′-OH group at the transposon terminus. Then the same active site is used to catalyze the joining of this 3′-OH terminus to a phosphate group on the opposite strand of the same end. This generates the transposon end hairpin and severs the final connection between the transposon and the flanking donor DNA in one chemical step. The hairpin end must then be cleaved to reex pose the 3′-OH group for joining to the target DNA in the final step. It is likely that a number of plant transposons also use this mechanism of excision. In the third excision mechanism, the transposase first makes a nick at only one transposon end. Then the exposed 3′-OH terminus is joined to a phosphate group on the same
Brenner’s Encyclopedia of Genetics, 2nd edition, Volume 7
DNA strand but just outside of the second end. This generates an excision intermediate in which the cleaved strand forms a covalently closed circle and the two transposon ends are held together by a single-strand bridge. Double-strand circles are generated from this by an as yet undefined mechanism. Then the transposase introduces a pair of single-strand cleavages at the abutting transposon ends. This opens up the circle gener ating a linear form of the excised transposon that can be directly inserted into a new target site. This mechanism is used by the bacterial transposon IS911 and other members of the IS3 family. It is not understood what constraints are responsible for the evolution of this seemingly complex exci sion pathway. Interestingly, the hairpin mechanism for transposon exci sion is also used in the formation of double-strand DNA breaks in V(D)J recombination. This is the process whereby antigen receptor genes are pieced together from separate coding seg ments in developing T and B cells in the immune systems of jawed vertebrates. Furthermore, the proteins that catalyze this double-strand break reaction, RAG1 and RAG2, have been shown to catalyze DNA transposition reactions in vitro via the hairpin mechanism. The use of a common mechanism for double-strand break formation in V(D)J recombination and bacterial DNA transposition suggests that the V(D)J recombi nation system evolved from an ancient bacterial transposon. It will be interesting to see if other mechanisms for carrying out transposon excision are used and what constraints favor these mechanisms.
See also: Insertion Sequences; Transposable Elements.
Further Reading Kennedy AK, Guhathakurta A, Kleckner N, and Haniford DB (1998) Tn10 transposition via a DNA hairpin intermediate. Cell 95: 125–134. McBlane JF, van Gent DC, Ramsden DA, et al. (1995) Cleavage at a V(D)J recombination signal requires only RAG1 and RAG2 proteins and occurs in two steps. Cell 83: 387–395. Sarnovsky RJ, May EW, and Craig NL (1996) The Tn7 transposase is a heteromeric complex in which DNA breakage and joining activities are distributed between different gene products. The EMBO Journal 15: 6348–6361. Ton-Hoang B, Betermier M, Polard P, and Chandler M (1997) Assembly of a strong promoter following IS911 circularization and the role of circles in transposition. The EMBO Journal 16: 3357–3371. Turlan C and Chandler M (2000) Playing second fiddle: Second-strand processing and liberation of transposable elements from donor DNA. Trends in Microbiology 8: 268–274.
doi:10.1016/B978-0-12-374984-0.01572-2
165