While the in vivo experiments described above provide considerable information about bacterial DNA replication, they do not shed much light on the cellular apparatus responsible for DNA replication. The best way to learn about the replication apparatus is to isolate it and then examine how each part works by itself and in concert with the other parts. This approach has been used to study the replication apparatus of viruses, bacteria, eukaryotes, and the archaea. Because the E. coli replication apparatus is probably the one that has been most thoroughly investigated, we begin by examining it. It is important to note that lessons learned from studying the E. coli replication apparatus appear to apply to the replication apparatus of other organisms.

    The replication apparatus is made of many different protein components that must be assembled on DNA before replication can begin. The first stage of DNA replication, initiation, involves the assembly of the replication apparatus at a unique site on the bacterial chromosome. Special proteins help to assemble the replication apparatus but do not participate further in the replication process. Initiation is followed by elongation, a process in which the leading strand is synthesized continuously and the lagging strand is synthesized discontinuously. A complex replication machine known as DNA polymerase Ⅲ holoenzyme is responsible for DNA synthesis during this stage. We will examine this replication machine in some detail. The final stage of replication, termination, begins when the two-replication forks meet about half way around the DNA molecule it also requires specific proteins.