Topoisomerase

Topoisomerase I solves the problem caused by tension generated by winding/unwinding of DNA. It wraps around DNA and makes a cut permitting the helix to spin. Once DNA is relaxed, topoisomerase reconnects broken strands (PDB 1a36)

Topoisomerases (type I: EC 5.99.1.2, type II: EC 5.99.1.3) are enzymes that unwind and wind DNA, in order for DNA to control the synthesis of proteins, and to facilitate DNA replication. The enzyme is necessary due to inherent problems caused by the double-helical nature of DNA, as first noted by Watson and Crick (Nature, May (171) 1953). The structure of DNA is a double-stranded helix, where the four bases, adenosine, thymidine, guanidine, and cytosine are paired and stored in the center of this helix. While this structure provides a stable means of storing the genetic code, Watson and Crick noted that the two strands of DNA are intertwined and this would require the two strands to be untwisted in order to access the information stored. However they also foresaw that there would be some mechanism to overcome this problem.

In order to help overcome these problems caused by the double helix, topoisomerases bind to either single-stranded or double stranded DNA and cuts the phosphate backbone of the DNA. This intermediate break allows the DNA to be untangled or unwound, and at the end of these processes, the DNA is reconnected again. Since the overall chemical composition and connectivity of the DNA does not change, the tangled and untangled DNAs are chemical isomers, differing only in their global topology, thus their name. Topoisomerases are isomerase enzymes that act on the topology of DNA.^[1]

Discovery

The need for this enzyme was recognized long before it was discovered. When the double-helical nature of DNA was determined by Watson and Crick, the authors noted that there must be some mechanism that would resolve the tangles that arise from this structural feature. The enzyme, originally termed gyrase, was first discovered by Harvard Professor James C. Wang.^[2]

Function

The double-helical configuration that DNA strands naturally reside in makes them difficult to separate, and yet they must be separated by helicase proteins if other enzymes are to transcribe the sequences that encode proteins, or if chromosomes are to be replicated. In so-called circular DNA, in which double helical DNA is bent around and joined in a circle, the two strands are topologically linked, or knotted. Otherwise identical loops of DNA having different numbers of twists are topoisomers, and cannot be interconverted by any process that does not involve the breaking of DNA strands. Topoisomerases catalyze and guide the unknotting of DNA by creating transient breaks in the DNA using a conserved Tyrosine as the catalytic residue.^[1]

The insertion of viral DNA into chromosomes and other forms of recombination can also require the action of topoisomerases.

Clinical significance

See also topoisomerase inhibitor

Many drugs operate through interference with the topoisomerases. The broad-spectrum fluoroquinolone antibiotics act by disrupting the function of bacterial type II topoisomerases.

Some chemotherapy drugs work by interfering with topoisomerases in cancer cells:

• type 1 is inhibited by irinotecan and topotecan.
• type 2 is inhibited by etoposide(VP-16), teniposide and HU-331, a quinolone synthesized from cannabidiol.

Topoisomerase I is the antigen recognized by Anti Scl-70 antibodies in scleroderma.

These small molecule inhibitors act as efficient anti-bacterial and anti-cancer agents by hijacking the natural ability of topoisomerase to create breaks in chromosomal DNA. These breaks in DNA accumulate, ultimately leading to programmed cell death, or apoptosis.

Topological problems

There are three main types of topology: supercoiling, knotting and catenation. Outside of the essential processes of replication or transcription, DNA needs to be kept as compact as possible and these three states help this cause. However when transcription or replication occur, DNA needs to be free and these states seriously hinder the processes. In addition, during replication, the newly replicated duplex of DNA and the original duplex of DNA become intertwined and need to be completely separated in order to ensure genomic integrity as a cell divides. As a transcription bubble proceeds, DNA ahead of the transcription fork becomes overwound, or positively supercoiled, while DNA behind the transcription bubble becomes underwound, or negatively supercoiled. As replication occurs, DNA ahead of the replication bubble becomes positively supercoiled, while DNA behind the replication fork becomes entangled forming precatenanes. One of the most essential topological problem occurs at the very end of replication, when daughter chromosomes must be fully disentangled before mitosis occurs. Topoisomerase IIA plays an essential role in resolving these topological problems.

Classes

Topoisomerases can fix these topological problems and are separated into two types separated by the number of strands cut in one round of action:^[3] Both these classes of enzyme utilize a conserved tyrosine, however these enzymes are structurally and mechanistically different.

• Type I topoisomerase cuts one strand of a DNA double helix, relaxation occurs, and then the cut strand is reannealed. Type I topoisomerases are subdivided into two subclasses: type IA topoisomerases which share many structural and mechanistic features with the type II topoisomerases, and type IB topoisomerases, which utilize a controlled rotary mechanism. Examples of type IA topoisomerases include topo I and topo III. Historically, type IB topoisomerases were referred to as eukaryotic topo I, but IB topoisomerases are present in all three domains of life. Interestingly, type IA topoisomerases form a covalent intermediate with the 5' end of DNA, while the IB topoisomerases form a covalent intermediate with the 3' end of DNA. Recently, a type IC topoisomerase has been identified, called topo V. While it is structurally unique from type IA and IB topoisomerases, it shares a similar mechanism with type IB topoisomerase.

• Type II topoisomerase cuts both strands of one DNA double helix, passes another unbroken DNA helix through it, and then reanneals the cut strand. It is also split into two subclasses: type IIA and type IIB topoisomerases, which share similar structure and mechanisms. Examples of type IIA topoisomerases include eukaryotic topo II, E. coli gyrase, and E. coli topo IV. Examples of type IIB topoisomerase include topo VI.

Both type I and type II topoisomerases change the linking number of DNA. Type IA topoisomerases change the linking number by one, type IB and type IC topoisomerases change the linking number by any integer, while type IIA and type IIB topoisomerases change the linking number by two.

References

Further reading

• James C. Wang (2009) Untangling the Double Helix. DNA Entanglement and the Action of the DNA Topoisomerases, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 2009. 245 pp. ISBN 9780879698799

See also

• DNA topology
• Supercoil
• TOP1
• Type II topoisomerase

External links

• MeSH DNA+Topoisomerases