(C) Alignment of the multimer resolution sites. The ArgR, FIS, XerC and XerD binding sites are boxed and conserved A-T stretches responsible for DNA bending are underlined. The -10 and -35 boxes of the ColE1 P cer promoter are underlined and the start of the Rcd coding region is indicated by an arrow. Nucleotides conserved

in at least 50% of the sequences are shown in bold and invariant sites are marked with an asterisk. It might be thought surprising that all multimer resolution sites of plasmids depicted in Fig. 1 are in the same orientation with respect to the replication origin (oriV). This is also true for all ColE1-like plasmids in Fig. 2A. The explanation for this observation may lie in the intimate association of replication control and multimer resolution in the stable maintenance of ColE1-like plasmids. Because all of the ColE1 replication origins in a cell buy MK-8776 function independently, plasmid dimers (which have two origins) replicate twice as often as monomers. As a result, dimers accumulate rapidly and clonally in a process known as the dimer catastrophe [25]. RNAI-RNAII copy number control counts origins rather than plasmids, so a dimer is not differentiated from two monomers. Consequently the copy number (i.e the number of independent molecules) of dimers is approximately half that of monomers.

ColE1 lacks active MEK162 manufacturer partition, so plasmid stability requires the maintenance of a high copy number. As a result the copy number depression caused by dimer accumulation causes plasmid instability [26]. One part of the solution to this problem is the resolution of dimers or higher multimers to monomers by site-specific recombination. The multimer resolution site of ColE1 (designated cer, for ColE1 resolution) contains binding sites for the host-encoded recombinase

XerCD and the accessory protein ArgR (Fig. 2C). They act together with PepA (whose binding site is less clearly defined) to convert dimers to monomers by site-specific recombination [27–30]. Conserved A-T tracts phased at approximately 10.5 bp intervals facilitate the curvature of the region between the ArgR and XerC/XerD binding sites, which is thought to be beneficial for recombination complex formation [31, 32]. These sequence elements ioxilan are conserved in the mrs sites of the ColE1-like plasmids (Fig. 2C). Multimer resolution is necessary but not sufficient to combat the threat of the dimer catastrophe. A checkpoint, mediated by the small regulatory transcript Rcd, ensures that the cell does not divide before multimers have been resolved completely to monomers [33]. Rcd binds to the enzyme tryptophanase, stimulating the production of indole which inhibits cell division by an unknown mechanism [34]. Rcd is expressed from the P cer promoter within cer. P cer is active in plasmid multimers but is repressed in monomers by FIS and XerCD [35]. A FIS binding site important for regulation of P cer has been mapped recently [35] (Fig. 2C).