Snyder and Champness Molecular Genetics of Bacteria. Tina M. Henkin
and chromosome translocation with FtsK. The two daughter chromosomes that have been replicated are indicated by light and dark blue lines, and the unreplicated portion of the chromosome is shown in gray. Unwinding of the template DNA strands that is associated with DNA replication twists the newly replicated strands of DNA, forming precatenanes that go on to become catenanes if not unlinked by the action of Topo IV. Topo IV can interact with the chromosome condensation protein MukB to remove catenanes before DNA is condensed. Topo IV also interacts with the FtsK translocase to coordinate decatenation with chromosome segregation. The replisome is shown as a yellow circle, and double-stranded DNA is shown as a single line for simplicity.
The condensin of E. coli, called MukB, was found because mutations in its gene interfere with chromosome segregation. MukB was suspected of condensing the DNA because the protein and supercoiling of the DNA can compensate for each other in allowing proper segregation of the daughter chromosomes into daughter cells. As indicated above, supercoiling can lead to the formation of precatenanes and catenanes that are removed by Topo IV. The removal of precatenanes and catenanes also appears to be regulated with the condensation of chromosomes by an interaction between one of the Topo IV subunits and MukB (Figure 1.19) (see Hayama and Marians, Suggested Reading). MukB interacts with DNA through association with the partner proteins MukF and MukE. B. subtilis also has a condensin, which is more similar in amino acid sequence to the eukaryotic condensins and so was also named SMC protein (see Britton et al., Suggested Reading). It also has partner proteins named ScpA and ScpB. In B. subtilis, the link between chromosome condensation and partitioning is becoming clearer with the finding that proteins that directly recognize the region around the origin and are involved in partitioning are able to recruit the condensin SMC in this organism (see Thanbichler, Suggested Reading).
Supercoiling
Another way bacteria condense DNAs is through supercoiling. In bacteria, all DNAs are negatively supercoiled, which means that DNA is twisted in the opposite direction to the Watson-Crick helix, creating underwinds. As discussed in more detail below, the underwinds introduce stress into the DNA, causing it to wrap up on itself, much like a rope wraps up on itself if the two ends are rotated in opposite directions. This twisting occurs in loops in the DNA, causing the DNA to be condensed into a smaller space.
KEEPING NEW SISTER CHROMOSOMES SEPARATE INVOLVES COORDINATING MULTIPLE PROCESSES
Many processes ensure that the chromosomes are physically separate, yet are gathered together in a manageable way in the bacterial cell. With circular chromosomes, an uneven number of recombination events will regularly form dimer chromosomes, where the two circles join to form one large circle that cannot be subdivided into daughter cells. The highly controlled process of dimer resolution with XerC, XerD, and FtsK in E. coli ensures that dimer chromosomes are kept separate without accidently making dimers out of separate chromosomes before they can be passed to the daughter cells. Circular chromosomes can also become conjoined like the rings on a chain that cannot be passed on to daughter cells. Another highly regulated process by Topo IV removes these links between the chromosomes. Regulation of Topo IV activity with condensation and FtsK transport, as shown in Figure 1.19, plays an important role in making sure the enzyme separates interlinked chromosomes and does not link them together. A number of processes compact the chromosomes in bacteria. Condensins gather regions of the chromosome together that are, in turn, held together by a number of nonspecific DNA-binding proteins to allow compaction of the bacterial chromosome. This process is facilitated by supercoiling that allows the chromosome to twist around itself. In the next section, we learn how chromosomes are efficiently partitioned into each daughter cell during the process of cell division.
CHROMOSOME PARTITIONING
Not only must the two daughter chromosomes be segregated after replication, they also must be segregated in such a way that each daughter cell gets only one of the two copies of the chromosome. Otherwise, one daughter cell would get two chromosomes and the other would be left with no chromosome and eventually would die. The apportionment of one daughter chromosome to each of the two daughter cells is called partitioning. Daughter cells that lack a chromosome after division are very rare, indicating that partitioning is a very efficient process in bacteria. Because of the importance of chromosome segregation, redundant mechanisms may have evolved to ensure that it occurs accurately. Indeed, many of the mechanisms that allow condensation of chromosomes can contribute to partitioning once the origin regions are located in the nascent daughter cells. While broad themes that describe partitioning across all bacteria have eluded our understanding, some important model systems are fairly well understood. In this section, we discuss what is known in the model bacteria.
The Par Proteins
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