6.10: DNA Topoisomerases

Topoisomerases are enzymes that relax overwound DNA molecules during various cell processes, including DNA replication and transcription. These enzymes regulate positive and negative DNA supercoiling without changing the nucleotide sequence. DNA overwinding in a clockwise direction results in positively supercoiled DNA, whereas underwinding in a counterclockwise direction produces negatively supercoiled DNA.

Types and Mechanism of action

Topoisomerases are divided into two main types. Type I Topoisomerases act on one strand of double-stranded DNA, and they are further divided into three categories: IA, IB, and IC. Type IA forms a covalent bond with 5' end of the cleaved DNA strand and removes negative supercoils. It creates a single-strand breakthrough which the opposite strand can pass, resulting in a locally untangled DNA molecule. Type IB forms a covalent bond with the 3' end of the broken DNA strand and can relax both positively and negatively supercoiled DNA. The enzyme rotates the cut single-strand around the opposite strand, untwisting the DNA in the process. Type IC is mainly found in archaea and has a similar mechanism as type IB. Most Type I topoisomerases do not require ATP to relax supercoiled DNA. With the exception of reverse gyrase, this unique type IA topoisomerase does require ATP and generates positive DNA supercoils rather than unwinding them.

Type II topoisomerases are ATP-dependent enzymes that cut both strands of a DNA double helix. They are divided into two subtypes, Type IIA and Type IIB. These subtypes are distinguished by their structure and locations of their protein domains. Both subtypes have similar mechanisms; they transfer a loop of intact supercoiled DNA through the broken double-strand, thereby untangling the coil by one loop. Bacterial gyrase, which belongs to the Type IIA topoisomerases, can introduce negative supercoiling in the DNA and thus is different from all other known topoisomerases.

The unwinding of the DNA double helix during replication results in overwinding in regions ahead of the replication fork. 

Additionally, supercoiling can occur when the DNA twists back on itself due to the inability of the DNA ends to freely rotate to relieve the torsional stress. This twisting inhibits further unwinding of the DNA, stalling vital cell processes such as DNA replication. 

To deal with this winding problem, cells have enzymes known as topoisomerases that have both nuclease and ligase activity; that is, these enzymes reversibly break then reconnect phosphodiester bonds in DNA to remove torsional strain in overwound DNA.

Topoisomerases fall into two categories. 

Type I topoisomerases are ATP-independent and act by cutting a bond between nucleotides on a single strand of double stranded DNA. 

The unbroken DNA strand is then passed through the gap in the broken strand into the upper cavity of the enzyme. 

Finally, the enzyme ligates the broken ends of the DNA strands back together and produces a locally relaxed DNA molecule.

Type II topoisomerases, on the other hand, are ATP-dependent and act on supercoiled DNA where the DNA is tangled around itself. 

The enzyme creates a double strand break in one loop of the DNA double helix before helping the unbroken loop to pass through this break via an ATP-dependent reaction.

Then, using the energy from a second ATP, Type II topoisomerase reseals the broken ends of the DNA strands and finally detaches from the DNA- leaving behind an untangled DNA helix.