Role of Topoisomerase 1 and 2 in DNA Replication

Topoisomerases are essential nuclear enzymes that play crucial roles in DNA replication, chromosome segregation, transcription, recombination, etc. These enzymes are present in every cell. Topoisomerases exist in two forms. 

• Topoisomerase 1(I)
• Topoisomerase 2 (II)

Topoisomerase 1 and 2

Topoisomerase 1

Topoisomerase 1 (Topo 1) is the simpler of the two. 

• This enzyme can cut only one strand of the DNA.
• It is seen in both prokaryotes and eukaryotes.
• A cut or nick caused by this enzyme causes the DNA molecule to rotate around its phosphodiester bond on the uncut strand.
• It is a single-chain polypeptide acting as a monomer.
• It relaxes a supercoiled DNA and unwinds it during replication.
• Topo 1 can relax the supercoiled DNA due to transcription as well.
• Cleavage by Topo 1 does not require ATP.
• It is not a cell cycle-dependent enzyme.

Topoisomerase 1 is further classified into three: IA, IB, and IC 

TopA or IA

It consists of bacterial and archaeal topoisomerases and topoisomerase III, another type of IA enzyme seen in E. coli. 

• IA causes a transient cleavage on one strand of supercoiled DNA, creating a 5′ – phosphotyrosyl intermediate.
• Topo III can unknot and decatenate the nicked or single-stranded DNA.

TopB or IB

TopIB can convert the DNA from a nicked to a religated state or vice versa. 

• It can relax both negative and positive supercoils.
• TopIB engages the DNA duplex as a C-shaped protein clamp that hinders DNA swiveling.

IC or Topoisomerase V

IC is structurally different from other Topo 1 enzymes but functionally close to the TopB enzyme. It is an archaebacterial enzyme binding to the 3’ end of the DNA strand. 

Topoisomerase 2

Topoisomerase 2 (Topo 2) enzymes can invade both strands of the DNA. It is seen in bacteria and eukaryotes. 

• It is a dimer, and the gene for this enzyme is identified as gyrA.
• Topo 2 can relax the DNA and can rejoin the strands.
• Eukaryotic Topo 2 is are homodimer, and in prokaryotes, they are heterodimers.
• These enzymes are responsible for DNA segregation and the maintenance of chromosome structure.
• The catalytic activity of Topo 2 requires energy and is dependent on ATP hydrolysis.

The enzyme will bond to the cleaved strand using a covalent bond and provide energy to the phosphodiester bond. When the DNA strand relaxes, this energy is used by the enzyme to reseal the strand. 

Topo 2 can be further classified into IIA and IIB. 

Type IIA

The IIA type of Topo2 includes three types.

• DNA Gyrase
• Eukaryotic topoisomerase II
• Bacterial topoisomerase IV

Type IIB

Type IIB topoisomerases consist of TopoVI in plants and Spo11 homologs, required to start double-strand cleavage that initiates recombination during meiosis. 

Topoisomerase Function In DNA Replication

Topoisomerase enzymes can alter the topology or shape of the DNA during replication. Some multicellular organisms have highly coiled DNA. Such supercoiled DNA poses difficulty during cell division and the replication process. 

Topoisomerase enzymes relax such supercoiled DNA and make it easier to separate the strands of a double-helix structure to form the replication fork.  

How Does it Work?

The coiled DNA, when untangled or unbound at one region, creates more tension in other areas. This tension could create tangles leading to a coiled DNA. The presence of topoisomerase enzymes prevents such tangling and eases the tension in the coiled areas. 

• Topoisomerases create small cuts or nicks in the tensed areas of DNA coils to unbind the tangles effortlessly.
• These enzymes are also capable of repairing these cuts during DNA replication.
• By performing such cuts and repairs during DNA replication, topoisomerases assist in creating a replication fork by cutting the strands and relaxing the other areas.
• It allows the double helix to rotate and reconnect the loose ends after replication.

Thus, topoisomerase 1 and 2 are essential enzymes that assist with this crucial step of DNA replication. 

References

• Burden, D., & Osheroff, N. (1998). Mechanism of action of eukaryotic topoisomerase II and drugs targeted to the enzyme. Biochimica et Biophysica Acta (BBA) – Gene Structure and Expression, 1400(1-3), 139-154. https://doi.org/10.1016/S0167-4781(98)00132-8
• Champoux, J. J. (1993). Mechanism of Catalysis by Eukaryotic DNA Topoisomerase I. Advances in Pharmacology, 29, 71-82. https://doi.org/10.1016/S1054-3589(08)60540-2
• Gaikwad, M., Konkimalla, V. B., & Salunke-Gawali, S. (2022). Metal complexes as topoisomerase inhibitors. Inorganica Chimica Acta, 542, 121089. https://doi.org/10.1016/j.ica.2022.121089
• Jaswal, S., Nehra, B., Kumar, S., & Monga, V. (2020). Recent advancements in the medicinal chemistry of bacterial type II topoisomerase inhibitors. Bioorganic Chemistry, 104, 104266. https://doi.org/10.1016/j.bioorg.2020.104266
• Nitiss, J. L. (2009). DNA topoisomerase II and its growing repertoire of biological functions. Nature Reviews. Cancer, 9(5), 327. https://doi.org/10.1038/nrc2608
• Shen, C. (2022). Nucleic acids: DNA and RNA. Diagnostic Molecular Biology (Second Edition), 1-26. https://doi.org/10.1016/B978-0-323-91788-9.00005-3
• Type II topoisomerase. (2024, September 12). In Wikipedia. https://en.wikipedia.org/wiki/Type_II_topoisomerase

Additional Topics

• Explain the Process of Transcription in Prokaryotes
• Transcription Mechanism in Eukaryotes
• Post-Transcriptional Modification of mRNA