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Early work concentrated on the functions of the so-called partitioning proteins, the products of the par genes. The Par functions were first discovered in plasmids, which are small DNA molecules that are found in bacterial cells and that replicate independently of the chromosome (see chapter 4). Because they exist independently of the chromosome, plasmids usually must also have a system for partitioning; otherwise, they would often be lost from cells during the process of division. The Par systems of plasmids are known to fall into two families, one represented by the Par system of plasmid R1 and the other, much larger family represented by plasmids P1, F, and many others. It is the second of these families to which the known Par functions of chromosomes belong. The molecular details of Par systems are addressed in chapter 4, but some of the basics are described here as they apply to chromosome segregation systems.

The region of DNA that is to be partitioned, whether it is the origin region of the chromosome or a plasmid, contains a series of cis-acting sites called parS sites (Figure 1.20). One of two proteins in this system, ParB, binds to the parS sites. Partitioning of the ParB-bound parS DNA occurs because it is attracted to the other protein component of the system, active ParA*, which binds DNA. ParA* binds DNA nonspecifically and basically coats the entire nucleoid. The system works because ParB-parS is attracted to DNA-bound ParA*, but upon interacting with ParA* it helps to convert the ParA* into inactive ParA that does not bind DNA and is therefore released from the chromosome. As ParB-parS follows the gradient of ParA* across the nucleoid, it keeps the two oriC regions separate from one another. ParA eventually converts back to its active ParA* form and binds elsewhere on the nucleoid.

Figure 1.20 Model of how an origin region containing parS sites bound by the ParB protein is segregated by its attraction to DNA-bound ParA proteins (ParA*). Inactivation and displacement of ParA by the ParB-parS complex provide a mechanism to separate the origin region-containing ParB-parS complexes in the dividing cell.

Par functions in B. subtilis. The ParAB/parS system in B. subtilis provides some insight into how partitioning of oriC can work with condensation functions. In B. subtilis, the proteins analogous to the ParA and ParB proteins are called Soj and Spo0J, respectively. These names come from early genetic studies of B. subtilis sporulation, where spo0J was identified as a gene required for sporulation and soj was identified as a suppressor of spo0J. The parS sites close to the origin of chromosome replication (see Box 1.1) are bound by Spo0J(ParB), and these are pulled apart following the gradient to active Soj(ParA*), similar to what is shown in Figure 1.20. In B. subtilis, Spo0J(ParB) is capable of recruiting condensin protein SMC. Recruitment of SMC may play a critical role in organizing the chromosomes to help extrude the origin regions as they are gathered together with the SMC protein and other nonspecific DNA-binding proteins.