Bidirectional replication of the circular E. coli chromosome unwinds about 100,000 base pairs per minute. At 10 bp per turn, this is 10,000 turns of DNA per minute or over 160 per second. If there were nothing to relieve this stress, DNA would be a tangled mess in seconds. Relief of torsional stress is essential for DNA replication to occur. Topoisomerases are enzymes with a "swivel" mechanism that can relieve torsional stress.
There are two general classes of topoisomerases, type I and type II. Type I enzymes change the DNA linking number (see here for more on linking numbers) in units of 1, whereas type II enzymes change the linking number in units of 2. Figure 24.30 shows the reaction mechanism of a type I topoisomerase and Figure 24.31 shows the mechanism for a type II topoisomerase. E. coli contains four different topoisomerases. Topoisomerases I and III are both type I, whereas topoisomerase II (also called DNA gyrase) and topoisomerase IV are both type II.
DNA gyrase - plays the predominant role during replicative chain elongation. DNA gyrase both relieves stress ahead of the replication and introduces negative supercoils into newly synthesized DNA. The gyrase A subunit is the target for binding of nalidixic acid, an inhibitor of DNA replication. Novobiocin binds to the B subunit and inhibits ATP cleavage.
Topoisomerase IV - plays a critical role in completion of a round of replication. Figure 24.33 shows the types of topological interconversions catalyzed by type II topoisomerases and Figure 24.34 shows how Topoisomerase IV decatenates replication involving a circular template.
Type I topoisomerases (Topoisomerases I and III) - Bind to DNA and break one strand. The 5' end of the strand is immobilized by a covalent bond between the DNA phosphate and a tyrosine. Rotation of the 3' end is followed by resealing.