Structure and Function of the Bacterial Genome. Charles J. Dorman
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the 5′‐GATC‐3′ sites at the promoter that become hemimethylated following DNA replication (Bogan and Helmstetter 1997). The process of transcribing gidA and mioC is important for the initiation of chromosome replication at oriC (Bramhill and Kornberg 1988b; Theisen et al. 1993), at least under some circumstances (Asai et al. 1998; Bates et al. 1997; Lies et al. 2015).
Figure 1.6 The genetic neighbourhood of oriC in E. coli. Filled arrows represent the genes and an open rectangle indicates the position of oriC. DnaA represses the gidA gene transcriptionally through DnaA boxes that overlap the gidA promoter. The mioC gene is repressed by SeqA binding to hemimethylated versions of 5′‐GATC‐3′ sites at the promoter that are generated by DNA replication. The mioC promoter is also subject to stringent control via the (p)ppGpp alarmone and it is repressed by MraZ, a protein that has been linked to the control of cell division. The rsmG gene encodes a methyltransferase for the modification of 16S rRNA (see Benítez‐Páez et al. 2012). The asnC gene encodes a HTH‐motif‐containing transcription regulator that is related to LRP and controls genes involved in asparagine metabolism (see Kölling and Lother 1985; Willins et al. 1991). Termination of transcription extending from asnC to mioC is dependent on a DnaA‐DNA complex at the asnC terminator, as described by Schaefer and Messer (1988).
1.4 Chromosome Replication: Elongation
Once replication has been initiated, the replisome is responsible for progressive DNA synthesis during the elongation phase of chromosome replication. This large complex is composed of a pentameric clamp loader, the DNA polymerase clamp (DnaN), the three‐subunit DNA primase (DnaG), and the hexameric helicase DnaB (Bailey et al. 2007; Reyes‐Lamothe et al. 2010) (Figure 1.4). The helicase uses ATP hydrolysis to unwind the DNA duplex, moving along the lagging strand of the DNA as it does so. Single‐stranded DNA‐binding protein (SSB) coats the separated ssDNA strands, thus preventing reformation of the duplex by religation and attack by nucleases (Beattie and Reyes‐Lamothe 2015).
The primase, DnaG, possesses a central RNA polymerase domain where the RNA primers used in DNA synthesis are manufactured (Corn et al. 2008). The primer emerges from the DnaG‐DnaB complex and is transferred to DNA polymerase and SSB (Corn et al. 2008). DNA Polymerase III works with the beta‐clamp protein (DnaN) to extend the primer, creating a new DNA strand at a rate of 1000 bases per second (Beattie and Reyes‐Lamothe 2015). It is advantageous to have DnaN as a component of the replisome because a beta‐clamp must be reloaded for the synthesis of each lagging strand Okazaki fragment (Beattie and Reyes‐Lamothe 2015). If the replication fork stalls or breaks, replication can be restarted through a DnaA‐independent mechanism. Here, the PriA helicase, in association with accessory proteins such as PriB, PriC, and DnaT, binds to the gapped replication fork and loads DnaBC. In some cases, the restart may be associated with a strong transcription promoter that generates an R‐loop where PriA can introduce DnaBC on the displaced DNA strand (Heller and Marians 2006; Kogoma 1997). Of the approximately 300 copies of DNA gyrase that are bound to the E. coli chromosome at any one time, about 12 accompany each moving replication fork to manage the DNA topological disturbance that is associated with fork migration (Stracy et al. 2019).
1.5 Chromosome Replication: Termination
Termination of DNA synthesis occurs within Ter, located at a point that is diametrically opposite oriC on the chromosome (Hill et al. 1987) (Figure 1.7). The Ter region has five copies of a 23‐bp DNA element on each flank and the 36‐kDa Tus protein binds to these sequences (Neylon et al. 2005). The Tus binding sites are asymmetric and have a permissive and a non‐permissive orientation (Figure 1.7). Replication forks can pass the Tus‐Ter nucleoprotein complexes when the DNA sequences are in the permissive orientation, but fork movement becomes arrested when the sequences are oriented in the non‐permissive direction. The mechanism of replication fork passage at Ter sites that are in the permissive orientation involves displacement of Tus by the DnaB helicase; when in the non‐permissive orientation, Tus prevents DnaB, and the replication fork, from translocating past that point (Bastia et al. 2008; Berghuis et al. 2015; Mulcair et al. 2006). Single‐molecule experiments performed in vitro have shown that the DNA also plays a critical role: in the non‐permissive orientation, the unwinding of the DNA by the approaching replication fork creates a powerful lock at the Tus‐Ter site that is an effective roadblock to further translocation by the fork; in the permissive orientation the lock does not operate and the fork can proceed (Berghuis et al. 2015).
Figure 1.7 Termination of chromosome replication in E. coli. (a) The moving replisome encounters an appropriately oriented Tus/Ter nucleoprotein complex and the interaction between Tus and the DnaB helicase halts replisome movement, leading to the termination of chromosome replication. (b) The 4.6 Mb chromosome of E. coli is shown, indicating the relative positions and orientations of the Ter sequences (grey arrowheads) with respect to one another and oriC and the tus gene. The black arrows on either side of oriC indicate the bidirectional nature of E. coli chromosome replication. Ter sites aligned with the direction of replication are in the permissive orientation and will allow the replication fork to pass; those oriented against the direction of fork movement are in the non‐permissive configuration and will halt fork movement if bound by Tus. The promoter of the tus gene overlaps the TerB sequence, resulting in negative autoregulation of tus transcription by the Tus protein. (c) An alignment of the DNA sequences of the Ter elements, showing the high degree of sequence conservation among the sites and the lack of dyad symmetry within each site. The latter feature ensures that the sites operate to stop forks moving in one direction only.
The newly synthesised DNA strand is unmethylated and forms one part of a hemimethylated duplex. For this reason, the products of chromosome replication are chemically distinct from the template duplex until a full methylation of the newly synthesised strand has taken place. DNA adenine methyltransferase, Dam, methylates DNA at 5′‐GATC‐3′ sites and there are 11 of these sites in oriC (Figure 1.2). The SeqA protein binds to these sites while they are still in their hemimethylated form, sequestering the origin and excluding DnaA (Han et al. 2003; Slater et al. 1995; von Freiesleben et al. 1994). The sequestered state persists for about one third of the cell cycle when it is relieved by dissociation of SeqA and methylation of the 5′‐GATC‐3′ sites by Dam (Kang, S. et al. 1999; Lu et al. 1994). SeqA also interferes with expression of the dnaA gene, reducing the levels of the DnaA protein available for binding to oriC (Campbell and Kleckner 1990). In addition, SeqA contributes to processes that ensure proper segregation of the chromosome copies at cell division (Helgesen et al. 2015; Waldminghaus and Skarstad 2009). It is interesting to note that both hemimethylated oriC and SeqA have been shown to associate with the cell envelope (Ogden et al. 1988; Slater et al. 1995), perhaps indicating a role for the complex in the positioning of oriC in the cell.
1.6 Replication Produces Physically Connected Products
The converging replication forks moving along the chromosome will create a topological problem as they approach one another in the Ter region. As chromosome replication comes to an end, the products that it generates will emerge as intertwined DNA duplexes. This physical linkage must be resolved if it is not to impede