Prokaryotic DNA Transposons: Classes and Mechanism


Transposition plays a major role in genome plasticity causing chromosome rearrangements, deoxyribonucleic acid (DNA) insertion and deletion mutations and is key in gene sequestration and transmission by horizontal gene transfer. The processes play important roles in genome evolution and function. Transposable elements (TR) can be classified according to the chemistry of the transposition process itself: the nature of the catalytic mechanisms involved in the DNA cleavages necessary to liberate a copy of the transposon from its donor DNA and DNA strand transfer events (involved in insertion into a target DNA).

This chapter is centred on prokaryotic TE, which use DNA intermediates for their movement. DNA transposable elements are extremely diverse, but, with a few exceptions, the mechanisms they use in their movement are common to both prokaryotic and eukaryotic TE.

There are only a limited number of enzyme types that carry out DNA transposition. They are DDE (DED), Y, S, Y1 (HUH), Y2 (HUH) transposases, names of which are based on the active‐site residues involved in catalysis. More recently, an additional class, the casposons, has been identified in archaea and bacteria, which use a different type of sequence‐specific endonuclease.

Transposition requires assembly of precise protein DNA complexes called transpososomes.

Key Concepts

  • Transposons are found in all living organisms.
  • Transposons are diverse in organisation.
  • Transposons use a limited number of enzyme types (transposases) for their movement.
  • Transposases catalyse DNA cleavage in the donor DNA molecule and DNA strand transfer into the target DNA.
  • Transposition requires an assembly of a precise protein–DNA complex, the transpososome.
  • Transpososomes are assembled through a strictly ordered series of events in which the DNA–protein interactions position the DNA for catalysis.

Keywords: transposase; nucleophilic attack; transpososome; assembly; catalysis

Figure 1. Cotranslational transposase binding. Transposases that catalyse IS movement often exhibit a strong preference for activity in cis in vivo. This figure shows that the IS911 transposase binding to an IS end occurs efficiently in the early stages of translation, while the N‐terminal DNA‐binding domain is emerging from the ribosome, but not at later stages. An RNA polymerase molecule (yellow form) in the process of transcribing the transposase gene while the following ribosome (grey form) translates the N‐terminal region of the transposase (thick yellow string). The emerging N‐terminal ribosome‐associated peptide is anchored close to the IS by the mRNA emerging from the RNApol transcription complex (thin black string). The emerging peptide is shown binding to the neighbouring double‐strand IS end (red cylinder). Binding occurs within a short window of time during translation but before the C‐terminus of the transposase has been synthesised (left of figure). The C‐terminal end is thought to mask the transposase N‐terminal DNA‐binding domain preventing binding of the full‐length protein (right of figure).
Figure 2. Trans cleavage. The figure shows a transposase dimer in a paired‐end complex with two transposon ends. Cleavage of single end is inefficient. Transposase bound at one end cleaves the other end. Cleavage therefore requires preassembly of the synaptic complex.
Figure 3. DDE catalysis. Only one of the relevant DNA strands is shown. Transposon DNA is shown in pink and flanking DNA in blue. The phosphodiester bond that undergoes cleavage in these reactions is shown as a chiral form. (a) Strand cleavage. Nucleophilic attack by a water molecule on the transposon phosphate backbone generates a 3′OH at the transposon end and a 5′phosphate on the donor flank. (b) Strand transfer. The 3′OH at the transposon end is then used as a nucleophile to attack the target DNA creating a phosphodiester link between the transposon strand and the target. A concerted attack of the opposite target strand by the 3′OH at the opposite end of the transposon would result in integration. The steps involving double‐strand donor and target DNA together with their polarity are presented on the right of this figure for clarity. (c) Although the chirality of the phosphate is not normally fixed, introduction of a sulphur atom to replace a nonbridging oxygen (O*) fixes one or the other chiral forms. In this case, the Rp form. (d) The one‐step in‐line nucleophilic attack, which leads to chiral inversion showing the proposed role of the DDE triad in positioning the required divalent metal ions. (e) The inverted Sp chiral form.
Figure 4. HUH catalysis. (a) The HUH endonuclease domain showing the catalytic tyrosine 127 and the triple of amino acids, which a divalent metal ion (M2+) required in catalysis. (b) Pentavalent transient enzyme DNA intermediate. (c) Covalent 5′ phosphotyrosine intermediate and releases the cleaved leaving group. This bond will subsequently be broken by nucleophilic attack using a suitable 3′ hydroxyl group.
Figure 5. Bacteriophage Mu. (a) Organisation. Mu is represented by a green box and its ends as red triangles. Only the relevant genes at the left end are shown. The transposase, MuA, binding sites for the at the left (L1, L2 and L3) and right (R1, R2 and R3) ends are shown underneath as blue boxes and white arrows indicating their relative orientation and spacing. The internal activating sequence or enhancer E is located towards the left end of the Mu genome (grey box) between divergent promoters for the repressor, MuC, and the early operon containing ner, MuA and MuB. It has a dual function as an operator sequence autoregulated by the repressor, MuC, and as an architectural component in assembling the Mu transpososome. It includes three MuC binding sites, O1, O2 and O3 and an essential IHF binding site. (b) Functional organisation of MuA. Iα: Enhancer binding domain; Iβ and Iγ: Mu end binding domain; IIα: DDE domain; IIβ IIIα: nonsequence specific nuclease domain; IIIβ: interaction with MuB and ClpX. (c) Transposition pathway. Mu DNA is shown as green, Mu end sequences as blue boxes, the enhancer as white, flanking DNA is black and target DNA is yellow. (A) Mu in a supercoiled donor molecule; (B) end alignment; the inset shows how the enhancer together with supercoiling establishes the correct architecture (topology), which involves binding of, and bending by, IHF (yellow circle) and HU (blue circle) and conveys MuA via the MuA enhancer binding domain. Operator sites, O1,2,3, left‐ and right‐end MuA binding sites, L1, L2 and L3 and R1, R2 and R3 are indicated; (C) the 4 MuA core; (D) stable synaptic complex, SSC, activation by MuB (+Mg2+,Mn2+ or Ca2+), underwinding of the Mu donor junction; (E) cleaved donor complex, CDC, MuA cleavage of the underwound junction (+Mg2+, Mn2+, Zn2+ or Co2+ NOT Ca2+); inset shows the target capture complex (TCC) with the relative positions of the various MuA domains of each of the 4 MuA monomers (red, pink, blue and light blue) and the relative positions of flanks (black) and target (yellow), orange star indicates position of one of the MuA active sites; (F) strand transfer complex (STC) in which both 3′OH at the cleaved Mu ends has been transferred into the target DNA molecule; (G) after strand transfer, both donor and target molecules are joined by a single‐strand bridge leaving 3′OH groups on the target, which can serve as primers in replication.
Figure 6. Tn7. (a) Organisation. Tn7 (∼14 000 bp) is shown as a green box and the ends as red triangles. Tn7 encodes five genes, tnsA, tnsB, tnsC, tnsD and tnsE, required for transposition shown as purple‐filled arrows together with a set of passenger genes (red‐filled arrow). A more detailed cartoon of the end organisation is shown below: if it is composed of 4 closely spaced 22 bp TnsB binding sites at the left end (blue arrows) and 3 more spaced out copies at the right end. (b) Organisation of the Tn7 transposition proteins. The schema indicates the relative position of regions involved in protein–protein interactions, DNA binding and catalytic domain (where known). (c) Tn7 transposition pathways. The figure shows a Tn7 copy infecting a naïve cell using TnsA, TnsB, TnsC and TnsD. TnsD binds to a region in the glmS gene and TnsAB direct cleavage at the attTn7 site outside the gene. Once established, Tn7 then uses TnsA, TnsB, TnsC and TnsE for insertion into replication forks or other structures with 3′ recessed DNA ends. It also interacts with the sliding clamp, DnaN, protein. Adapted from Peters, J.E. 2014 Tn7. In Mobile DNA III. Craig Nancy, L., Rice, P., Lambowitz, A., Gellert, M., and Sandmeyer, S.B. (eds). Washington DC: ASM Press.
Figure 7. Transposition of IS10 and IS50. (a) Compound transposons Tn10 and Tn5. Tn5 (5818 bp) carries flanking inverted copies of IS50 (1534 bp); Tn10 (9147 bp) carries flanking inverted copies of IS10 (1329 bp); Tpase: transposase gene; kan, tet, ble, str: resistance genes for kanamycin, tetracycline, bleomycin and streptomycin, respectively. OE and IE: Outside and inside ends of the component IS with respect to the compound transposons. *Indicates GATC DAM methylation sites in the IS ends. The transcription units in the right IS50 encode the transposase (Tpase) and an inhibitor (Inh) protein, respectively. The outward facing arrow in the left IS50 indicates the presence of a promoter, which drives expression of the kan gene resulting from IS50 mutation. Transcription units of the right IS10: RNA‐IN transposase mRNA; RNA‐OUT, highly structured antisense regulatory RNA, which pairs with the 5′ end of RNA‐IN and sequesters the ribosome binding site and the Tpase start codon. (b) Transposition of IS10 and IS50. This involves formation of a tight DNA hairpin at the TE ends. The DDE Tpase first catalyses 3′ end hydrolysis to generate a 3′OH. This is then used as a nucleophile to attack the opposite strand shedding both donor flanks. The Tpase then catalyses hydrolysis of the hairpin to produce free 3′OH ends, which then continue on to attack the target DNA. (c) Active site structure of the IS50 Tpase. Based on Steiniger et al. , a view of contacts between Tpase and bases at the end of IS50. DNA is in blue, Tpase is shown in a variety of colours. Both transferred and nontransferred strands are shown. A 3′OH is shown at the tip of the cleaved transferred strand (3′OH‐GACT). There is also a 5′OH on the nontransferred strand. This is because an artificial substrate with a 5′OH rather than the phosphate was used to obtain the cocrystals. Catalytic triad residues (D) Asp97, (D) Asp188 and (E) Glu326 together with other key amino acids are shown. The figure illustrates the ‘flipped‐out’ T of the 5′‐CTGA tip of the nontransferred strand and its stacking with a tryptophan (W298) residue. (d) One pathway of IS10 transposon assembly. Transposon DNA is shown in green and the tips are represented by green‐filled arrowheads. Flanking DNA is grey, and target DNA is represented in light green. A Tpase dimer is shown as red and pink ovals bound to each transposon end. The figure shows (A) a ‘bent’ paired‐end complex (b‐PEC) in which one of the two arms is, in this case the α arm, is constrained by binding of IHF (yellow circle); (B) cleavage of one end occurs to generate the single‐end break complex (α‐SEB); (C) HNS (blue circle) is recruited to the opposite end and facilitates removal of the IHF protein in α‐SEB to form an unfolded SEB (uf‐SEB); (D) cleavage at the other end generates a double‐end break complex (uf‐DEB); (E) target DNA is then recruited to form the target capture (TCC)/strand transfer (STC) complex. In the absence of HNS, it is thought that IHF remains in the (D) and (E) complexes and that the bent configuration imposed by IHF can favour intramolecular insertion into either Tn10 itself or into neighbouring donor DNA.
Figure 8. IS911 Transposition. (a) Organisation. IS911 (1250‐bp) is shown as a green box. The red triangles at each end represent the left (IRL) and right (IRR) terminal inverted repeats. The two open reading frames, orfA (light purple) and orfB (purple), are positioned in The relative reading phases 0 and −1, respectively. An indigenous promoter, pIRL, partially located in IRL (not shown), drives their expression. The region of overlap between orfA and orfB includes translational frameshifting signals to produce OrfAB (not shown). The two proteins, OrfA and OrfAB, are shown below. The position of the helix‐turn‐helix (HTH) motif involved in recognition of and binding to the IS ends is shown as a small light box. A leucine zipper (LZ) motif with 4 heptad repeated elements involved in homo‐ and hetero‐multimerisation of OrfAB and OrfA is indicated at the end of OrfA and at the frameshift junction of OrfAB. Note that frameshifting occurs within the last heptad to regenerate a heptad of different sequence. This presumably allows a distinction to be made between hetero‐ and homomultimers. A second region, M, necessary for OrfAB multimerisation is shown, as is the catalytic core of the enzyme that carries a third multimerisation domain. OrfAB translation terminates within the right IR. (b) Transposon excision. (A) Donor plasmid carrying the insertion sequence. The transposon is shown in green with red IR, the flanking in donor DNA in white and the target DNA in black. (B) Formation of the first synaptic complex, the paired‐end complex (PEC). (C) Cleavage of the left or right inverted repeat (IR) and attack of the opposite end. (D) Formation of a single‐strand bridge to create a figure‐eight molecule if the donor is a plasmid. (E) The product of IS‐specific replication using the 3′OH generated on the donor DNA: the double‐strand circular IS transposition intermediate and the regenerated transposon donor plasmid. (c) Integration. (F) Formation of a second synaptic complex and engagement of the target DNA (black). (G) Cleavage of the IS circle generating one 3′OH at each IS end. (H) Integration using staggered attack on the target. (I) The newly integrated IS after repair to form the target repeat (black).
Figure 9. IS608 Transposition. (a) Organisation. Left (red, LE) and right (blue, RE) ends with subterminal transposase recognition hairpins (HP). Left and right cleavage sites are presented as red and blue boxes, respectively. The boxed tetranucleotides at the 5′ end of the hairpins are the guide sequences that interact on the left with the black tetranucleotide TTAC cleavage site, which does not belong to the IS and is also the IS insertion target sequence, and on the right with the right IS end. The base interactions are indicated by blue arrows. (b) Transposition excision pathway. (A) Inactive form of TnpA dimer in the absence of DNA. Green, orange ovals and dark green and orange cylinders represent the body and the arms of the two monomers, respectively. At the ends, dotted red and blue lines represent 19 nucleotide linker at the left end (LE) (see A) and the 10 nucleotide linker at the right end (RE), light red and light blue boxes represent the left and right guide sequences, respectively. (B) TnpA activation following binding of LE and RE resulting in (catalytic sites in trans). (C) Cleavage of both ends forms a 5′ phosphotyrosine linkage between the catalytic tyrosine, Y127, and LE on one arm (dark orange cylinders) and between Y127 and the RE flank on the other (dark green cylinders). 3′‐OH groups are shown as yellow circles. Reciprocal rotations of both arms from trans to cis configuration are shown by unfilled black arrows. (D) Strand transfer takes place to reconstitute the joined donor backbone (donor joint) and generate the RE–LE transposon junction. The single‐strand IS DNA circle and donor joint is then released. The relationship between the replication fork and the excision process is shown in the cartoons on the right of the panel. Points of cleavage are indicated by small black arrows. The large unfilled arrowhead indicated the direction of replication. (c) Transposition insertion pathway. (E) Reset: transition from cis to trans configuration. (F) Target site engagement. (G) Cleavage of the RE–LE junction and target and transition from trans to cis configuration. (H) Regeneration of the left and right transposon ends.


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Chandler, Michael(Sep 2017) Prokaryotic DNA Transposons: Classes and Mechanism. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0000590.pub2]