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During the process of DNA replication, two circular daughter chromosomes will periodically become joined, forming a chromosome dimer, in which they are joined end to end to form a double-length circle. Dimer chromosomes can result from recombination between the two replicating chromosomes and are fairly common. Recombination involved in restarting stalled DNA replication forks from a sister chromosome probably accounts for many of these events (see chapter 9). Such dimers prevent chromosome segregation because the two daughter chromosomes are part of the same large molecule.

If dimer chromosomes can be created by recombination, they can also be resolved into the individual chromosomes by a second recombination event. The general recombination system could in theory resolve the dimers between sister chromosomes by recombination; however, the general recombination system can both create and resolve dimers, depending on how many crossovers occur between the daughter DNAs. An odd number of crossovers occurring between any two sequences on the two daughter DNAs in the dimer will resolve the dimer, but an even number of crossovers will recreate a dimer.

All bacteria with a circular chromosome appear to have a system dedicated to dimer resolution. In E. coli, and in most bacteria, the so-called Xer recombination system is used to resolve chromosome dimers. Rather than using the general recombination system, the Xer systems involve a site-specific recombinase (see chapter 8) to resolve chromosome dimers. This system has evolved so that it resolves dimers into the individual chromosomes but does not create new dimers. Its action is also coordinated with division of the cell and other important chromosome-partitioning functions. The Xer recombination system consists of two proteins called XerC and XerD and a specific site in the chromosome called dif. If two copies of the dif site occur on the same DNA, as happens when the chromosome has formed a dimer, the Xer proteins promote recombination between the two dif sites, resolving the dimer into the individual chromosomes (Figure 1.17). The dif site is always found centrally located in the ter region in bacterial chromosomes. This is likely, in part, to help ensure that there is only one dif site in the cell until just before cell division so that it is not replicated until just before the chromosome has completed replication and just before the cell divides. As added insurance, the activity of the Xer site-specific recombination system is also dependent on the formation of the division septum through an interaction with the FtsK protein. As diagrammed in Figure 1.17, FtsK protein is localized to the region where the division septum pinches in during cell division, where it plays multiple roles, including facilitating dimer resolution. While the Xer proteins are needed for dimer resolution, they are actually active for full dimer resolution only when they interact with FtsK. As shown in Figure 1.17, the localization of FtsK at the septum limits the dimer resolution process temporally and spatially to when the daughter chromosomes are in the process of moving through the septum into daughter cells, a process that is facilitated and coordinated by FtsK itself (see below) (see Aussel et al., Suggested Reading).

The FtsK protein is a DNA translocase that can pump DNA through itself to help align the two dif sites in a dimer chromosomal DNA at the septum in the middle of the cell before they recombine, thereby facilitating segregation into daughter cells (Figure 1.17). See the reconstructed image of the structure of the motor domain of FtsK at the start of this chapter (see also Jean et al., Suggested Reading). An obvious question is how the FtsK protein “knows” which direction pumps to engage for transporting DNA in the correct direction to move a dif site to the septum. It does this by using sites on the DNA as an orientation cue. These sites are called the KOPS sites, for FtsK-orienting polar sequence. Polar means that they read differently in one direction on the DNA than in the other. These sequences are oriented in the DNA so that they will only be read progressing from the origin to the dif site in the chromosome; the FtsK protein, by translocating the DNA in the direction pointed to by the KOPS sites, will pump the DNA toward the dif sites close to the terminus of replication. Note in Figure 1.17 how the polar KOPS sites in the chromosome (shown as half-arrows) can be used as directional information by FtsK to mobilize the chromosome to the daughter cells while moving the dif sites toward the septum. This is just one example of how the chromosome, typically thought of as the informational storehouse of the cell, also contains structural information used by the many proteins that manage and repair the chromosome (Box 1.1). FtsK also has a domain that interacts with topoisomerase IV, a protein capable of untangling catenanes in the chromosomes (see below). Therefore, the FtsK protein coordinates a veritable clearinghouse of activities that help with chromosome management during chromosome replication and chromosome segregation.

Figure 1.17 Model of the way in which chromosome translocation by FtsK coordinates chromosome segregation with dimer resolution. The two daughter chromosomes in a dimerized chromosome are shown in different shades of blue for emphasis. (A) Three possible distributions of the newly replicated dimer chromosome are shown following the start of cell septation. FtsK is a DNA translocase that can pump the chromosomes to the correct daughter cells using polar sequences in the chromosome called KOPS sites (shown as half arrows) while also moving the dif sites into alignment at the septum. Green indicates FtsK complexes that are actively pumping; orange indicates idle FtsK complexes where activity is set by the orientation of KOPS sites. (B) After aligning the dif sites, the FtsK protein also interacts with the XerCD enzyme, allowing it to resolve the dimer chromosomes at the dif sites. (C) The coordinated activities of the dimer resolution system and FtsK lead to monomer chromosomes that are capable of full segregation to daughter cells. From Camara JE, Crooke E, in Higgins NP (ed), The Bacterial Chromosome (ASM Press, Washington, DC, 2005).

Homologs of FtsK are widespread, and a homologous protein called SftA appears to carry out similar functions in B. subtilis (see Biller and Burkholder, Suggested Reading). Some bacteria have more than one FtsK-like protein, presumably for other specialized tasks. In the case of B. subtilis, another FtsK homolog, SpoIIIE, is responsible for translocating the final third of the chromosome into spores during spore development so the spore will get a complete copy of the chromosome (see chapter 12). How the roles of FtsK, SpoIIIE, and SftA differ and how the multiple members are involved in various DNA processing events in a single cell remain active areas of research with many questions still to be answered.

Interestingly, instead of XerC and XerD, Streptococcus and Lactococcus species have a system more closely related to bacteriophage integration systems that uses a single protein called XerS to carry out the same function (see Le Bourgeois et al., Suggested Reading). Archaea also seem to use a single protein (in this case called XerA) to resolve dimer chromosome at a cis-acting dif site (see Cortez et al., Suggested Reading). The regulation of dimer chromosome resolution in these systems and any involvement of FtsK-like proteins are unclear.

Figure 1.18 Model of the way in which unwinding of the template DNA strands can cause twists that can diffuse across the replication complex and twist the new DNA strands. (A) The replication machinery must open the double-stranded DNA to copy the template strands. (B) Unwinding the template DNA strands introduces twists (shown by thin red arrows) called positive supercoils ahead of the replication fork. (C) Some of the torsion that is generated ahead of the replication fork can be relieved by rotation of the replication complex itself. The torsional stress can spread behind the fork and intertwine the new copies of the chromosome (shown by a thick red arrow). The intertwined chromosomes are called precatenanes. (D) Precatenanes result in links in the daughter chromosomes called catenanes that must be unlinked for the chromosomes to separate into daughter cells.