Figure 1. Two transposition pathways. (a) Replicative ‘cointegrate’ pathway. 3¢-OH groups are denoted by arrowheads, and 5¢ phosphate groups by filled circles. The two target DNA phosphodiesters that will be attacked by transposon ends during strand transfer are shown already cleaved, for clarity. The short lines connecting the two DNA chains in the target represent the characteristic sequence duplicated after transposition. Wavy arrows denote alternative processing of the branched intermediate. Recombination between duplicated TEs in the cointegrate is signified by a cross. (b) Conservative ‘cut-and-paste’ pathway. All symbols as in (a).

Figure 2. Adjacent deletions and inversions produced as a consequence of intramolecular ‘cointegrate’ events. (a) Deletions; a–d represent genetic markers in the donor replicon. Following cleavage and strand transfer, replication of the branched intermediate produces two replicons, one deleted for markers c–d and the other for markers a–b flanking the original transposon. (b) Inversions; as in (a), except that opposite DNA strands are used as target in the strand transfer step. Replication of the branched intermediate produces inversion of markers a–b with respect to c–d. Symbols as in Figure 1.

Figure 3. Essential DNA and protein components of Mu transposition. (a) AttL, attR and enhancer regions encompass multiple DNA sites essential for transposition. Cleavage and strand transfer occurs at specific nucleotides (diamonds) outside L1 and R1, at the junction of Mu and non-Mu DNA. (b) Domain structure of transposase MuA. Of the three major proteolytic fragments or domains, I binds to sites in the enhancer and I to sites in attL and attR. Domain II has the catalytic DDE residues. Domain III is essential for assembly of the transpososome, as well as for interaction with the allosteric regulator MuB. Amino acid numbers are indicated below the protein structure.

Figure 4. Nucleoprotein complexes in the Mu transposition pathway. AttL, attR and the enhancer sequences are designated L, R and E, respectively.

Figure 5. Remodelling transposition complexes for Mu replication. The stable strand transfer complex (type II-1; see Figure 4) is first destabilized by ClpX (type II-2), allowing displacement and exchange of MuA with a host factor MRF2 (type II-3), prior to entry of PolIII holoenzyme for Mu replication.

Figure 6. Formation of a hairpin intermediate during the cut-and-paste pathway of Tn10 transposition. Symbols as in Figure 1.