Читать книгу Snyder and Champness Molecular Genetics of Bacteria - Tina M. Henkin - Страница 66

As discussed above, the antiparallel configuration of DNA requires that the two DNA polymerases travel in two different directions while still allowing the larger replication machine to travel in one direction down the chromosome (Figure 1.8). This leads to fundamental differences in the natures of leading- and lagging-strand DNA replication. While replication of the leading-strand template can occur as soon as the strands are separated by the DnaB helicase, replication of the lagging-strand template is consistently reinitiated approximately every 1 to 2 kilobases (kb); this slows the process, hence the name lagging-strand synthesis. The short pieces of DNA produced from the lagging-strand template are called Okazaki fragments. Synthesis of each Okazaki fragment requires a new RNA primer about 10 to 12 nucleotides in length. In E. coli, these primers are synthesized by DnaG primase at the template sequence 3′-GTC-5′, beginning synthesis opposite the T. These RNA primers are then used to prime DNA synthesis by DNA polymerase III, which continues until it reaches the last RNA primer produced by DnaG (Figure 1.8). Before these short pieces of DNA that are annealed to the template can be joined to make a long, continuous strand of DNA, the short RNA primers must be removed. This process is carried out by DNA polymerase I using its flap exonuclease activity to displace and cleave the RNA strand (Figure 1.9). As DNA polymerase I displaces the RNA primer, it extends the upstream (i.e., 5′) DNA that was previously polymerized by DNA polymerase III (Figure 1.8). Ribonuclease (RNase) H may contribute to this process under some circumstances by using its ability to degrade the RNA strand of a DNA-RNA double helix (Table 1.1). The Okazaki fragments are then joined together by DNA ligase as the replication fork moves on, as shown in Figure 1.8. By using RNA rather than DNA to prime the synthesis of new Okazaki fragments, the cell likely lowers the mistake rate of DNA replication (see below).

What actually happens at the replication fork is more complicated than is suggested by the simple picture given so far. For one thing, this picture ignores the overall topological restraints on the replicating DNA. The topology of a molecule refers to its position in space. Because the circular DNA is very long and its strands are wrapped around each other, pulling the two strands apart introduces stress into other regions of the DNA in the form of supercoiling. If no mechanism existed to allow the two strands of DNA to rotate around each other, supercoiling would cause the chromosome to look like a telephone cord wound up on itself, an event that has been experimentally shown to eventually halt progression of the DNA replication fork. To relieve this stress, enzymes called topoisomerases work to help undo the supercoiling ahead of the replication fork. DNA supercoiling and topoisomerases are discussed below. The fork itself can also twist when the supercoiling that builds up ahead of the replication fork diffuses behind the replication fork, a process that twists the two new strands around one another and that is also sorted out by topoisomerases (see below).