Tn3 transposon

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The Tn3 transposon is a 4957 base pair mobile genetic element, found in prokaryotes. It encodes three proteins:

Contents

Tn3 is an example of replicative transposon (Copy-Pest type transposone).

Initially discovered as a repressor of transposase, resolvase also plays a role in facilitating Tn3 replication (Sherratt 1989).

The transposon is flanked by a pair of 38bp inverted repeats.

Mechanism of replication

Replicative integration. Blue arrow = Transposon, Green triangle = Endonuclease recognition site Replicative integration in Tn3 transposon.png
Replicative integration. Blue arrow = Transposon, Green triangle = Endonuclease recognition site

Step 1 – Replicative integration

This first stage is catalysed by transposase.

The plasmid containing the transposon (the donor plasmid) fuses with a host plasmid (the target plasmid). In the process, the transposon and a short section of host DNA are replicated. The end product is a 'cointegrate' plasmid containing two copies of the transposon.

Shapiro (1978) [1] proposed the following mechanism for this process:

  1. Four single-strand cleavages occur – one on each strand of the donor plasmid and one on each strand of the target plasmid.
  2. The donor and target plasmids are ligated together, but there are two single-stranded regions, due to the positioning of the original cleavages.
  3. DNA replication makes the single-stranded regions double stranded, using the existing strand as a template. It is in this stage that the transposon is replicated.
    N.B. Diagram is not intended as an accurate representation of 3D structure. Tn3 transposon replicative integration diagram.png
    N.B. Diagram is not intended as an accurate representation of 3D structure.

The diagrams on the right illustrate the way in which the positions of the cleavages lead to the replication of certain regions once the plasmids have fused.

Step 2 – Resolution

The reaction catalysed by Tn3 resolvase Homologous recombination in Tn3 transposon.png
The reaction catalysed by Tn3 resolvase

To separate the host and target molecules Tn3 resolvase executes site-specific recombination between the old and new copy of transposon at a specific site called res, which is present in each copy of the transposon. Res is 114 bp long and it consists of 3 sub-sites, namely sites I, II and III. Each of these sites is of different lengths (28, 34 and 25bp, respectively) and they are unevenly spaced with 22bp separating sites I and II and only 5bp between sites II and III. The sites consist of 6bp inverted repeat motifs flanking a central sequence of variable length. These motifs act as binding sites for resolvase, so that each site binds a resolvase dimer but with varying affinity and probably a slightly different protein-DNA complex architecture. [2] [3] All three sub-sites are essential for recombination.

At recombination, two directly repeated res sites with resolvase dimers bound to each sub-site, come together to form a large complex structure called the synaptosome. Resolvase bound to sites II and III initiates the assembly of this complex. In this structure, exact architecture of which is still unclear, two res sites are intertwined in such a way as to juxtapose two copies of site I, allowing resolvase dimers bound to each site to form a tetramer. Again, it is the interaction between the resolvase dimers bound at accessory sites (sites II and III) and resolvase at site I that causes the two dimers to synapse and form a tetramer. After the tetramer is formed it becomes activated and the top and bottom DNA strands are simultaneously cleaved in the middle of the site I with a 2bp overhang. The strand exchange ensues by as yet unknown mechanism with a resulting net rotation of 180°. The strand exchange is then followed by the religation (Stark et al., 1992). Recombination between two directly repeated res sites separates, or resolves, the "cointegrate" into two original molecules, each one now containing a copy of the Tn3 transposon. After resolution these two molecules remain linked as a simple two-noded catenane which can be easily separated in vivo by a type II topoisomerase (Grindley 2002). Wild type resolvase system absolutely requires a supercoiled substrate and that the recombination sites are oriented in a direct repeat on the same DNA molecule. However, a number of "deregulated" or "hyperactive" mutants that have lost the requirement for the accessory sites have been isolated. These mutants are capable of catalysing recombination between two copies of site I only, which basically reduces the recombination site size from 114bp to only 28bp. [4] [5] Furthermore, these mutants have no supercoiling or connectivity requirements (Arnold et al., 1999) and have been shown to work in mammalian cells. [6] Hyperactive resolvase mutants have so far proven useful in creating resolvases with altered sequence specificity [7] but also in structural work. [8]

The entire resolvase recombination reaction can be reproduced in vitro, requiring only resolvase, a substrate DNA and multivalent cations, using either wild type protein or hyperactive mutants. [4] [9]

Hyperactive resolvase mutants, if further developed, could become an alternative to Cre and FLP, the most commonly used recombination systems in molecular biology to date.

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DNA transposons are DNA sequences, sometimes referred to "jumping genes", that can move and integrate to different locations within the genome. They are class II transposable elements (TEs) that move through a DNA intermediate, as opposed to class I TEs, retrotransposons, that move through an RNA intermediate. DNA transposons can move in the DNA of an organism via a single-or double-stranded DNA intermediate. DNA transposons have been found in both prokaryotic and eukaryotic organisms. They can make up a significant portion of an organism's genome, particularly in eukaryotes. In prokaryotes, TE's can facilitate the horizontal transfer of antibiotic resistance or other genes associated with virulence. After replicating and propagating in a host, all transposon copies become inactivated and are lost unless the transposon passes to a genome by starting a new life cycle with horizontal transfer. It is important to note that DNA transposons do not randomly insert themselves into the genome, but rather show preference for specific sites.

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References

  1. Shapiro, James (April 1979). "Molecular model for the transposition and replication of bacteriophage Mu and other transposable elements". PNAS. 76 (4): 1933–1937. Bibcode:1979PNAS...76.1933S. doi: 10.1073/pnas.76.4.1933 . PMC   383507 . PMID   287033.
  2. Abdel-Meguid SS, Grindley ND, Templeton NS, Steitz TA (April 1984). "Cleavage of the site-specific recombination protein gamma delta resolvase: the smaller of two fragments binds DNA specifically". Proc. Natl. Acad. Sci. U.S.A. 81 (7): 2001–5. Bibcode:1984PNAS...81.2001A. doi: 10.1073/pnas.81.7.2001 . PMC   345424 . PMID   6326096.
  3. Blake DG, Boocock MR, Sherratt DJ, Stark WM (September 1995). "Cooperative binding of Tn3 resolvase monomers to a functionally asymmetric binding site". Curr. Biol. 5 (9): 1036–46. doi: 10.1016/S0960-9822(95)00208-9 . PMID   8542280.
  4. 1 2 Arnold PH, Blake DG, Grindley ND, Boocock MR, Stark WM (March 1999). "Mutants of Tn3 resolvase which do not require accessory binding sites for recombination activity". EMBO J. 18 (5): 1407–14. doi:10.1093/emboj/18.5.1407. PMC   1171230 . PMID   10064606.
  5. Burke ME, Arnold PH, He J, et al. (February 2004). "Activating mutations of Tn3 resolvase marking interfaces important in recombination catalysis and its regulation". Mol. Microbiol. 51 (4): 937–48. doi:10.1046/j.1365-2958.2003.03831.x. PMID   14763971.
  6. Schwikardi M, Dröge P (April 2000). "Site-specific recombination in mammalian cells catalyzed by gammadelta resolvase mutants: implications for the topology of episomal DNA". FEBS Lett. 471 (2–3): 147–50. doi: 10.1016/S0014-5793(00)01394-6 . PMID   10767411. S2CID   83750793.
  7. Akopian A, He J, Boocock MR, Stark WM (July 2003). "Chimeric recombinases with designed DNA sequence recognition". Proc. Natl. Acad. Sci. U.S.A. 100 (15): 8688–91. Bibcode:2003PNAS..100.8688A. doi: 10.1073/pnas.1533177100 . PMC   166373 . PMID   12837939.
  8. Li W, Kamtekar S, Xiong Y, Sarkis GJ, Grindley ND, Steitz TA (August 2005). "Structure of a synaptic gammadelta resolvase tetramer covalently linked to two cleaved DNAs". Science. 309 (5738): 1210–5. Bibcode:2005Sci...309.1210L. doi:10.1126/science.1112064. PMID   15994378. S2CID   84409916.
  9. Reed RR, Grindley ND (September 1981). "Transposon-mediated site-specific recombination in vitro: DNA cleavage and protein-DNA linkage at the recombination site". Cell. 25 (3): 721–8. doi:10.1016/0092-8674(81)90179-3. PMID   6269756. S2CID   28410571.