Topoisomerase: Structure, Types, and Functions

Topoisomerases are a class of enzymes that play a crucial role in DNA metabolism. Their primary function is to regulate the topological state of DNA by introducing temporary breaks in the DNA strands. 

This activity allows them to relieve the torsional strain that builds up during processes such as DNA replication, transcription, recombination, and chromosome condensation.

In the early 1970s, James C. Wang and collaborators made a significant breakthrough when they isolated an enzyme from Escherichia coli (E. coli) that was capable of introducing negative supercoiling into DNA molecules. They named this enzyme DNA gyrase and demonstrated its role in modulating DNA topology.

Topoisomerases are of two main types: Type I and Type II. Type I topoisomerases create transient breaks in one strand of the double helix DNA and pass another strand through the break before resealing it. 

Type II topoisomerases create transient breaks in both strands of the DNA double helix. They pass another double-stranded DNA through the break before resealing it.

Topoisomerases are essential for maintaining the structural integrity of DNA and ensuring proper cellular function. Inhibition of topoisomerase activity has been exploited as a strategy for cancer treatment, as many anticancer drugs, such as etoposide and doxorubicin, target these enzymes to interfere with DNA replication and cell division in rapidly dividing cancer cells.

Types of Topoisomerase

Topoisomerases are enzymes classified into two main types based on their mechanisms of action and the number of strands they cleave during their catalytic cycle.

Type I Topoisomerases

Type I topoisomerases are a class of enzymes involved in regulating DNA topology by introducing transient single-strand breaks in the DNA double helix. These enzymes are essential in DNA replication, transcription, recombination, and chromatin remodeling. Type I topoisomerases are further subdivided into two subclasses: Type IA and Type IB.

  1. Type IA Topoisomerases:
  • Type IA topoisomerases are characterized by their ability to change DNA topology by introducing transient single-strand breaks in one DNA strand.
  • These enzymes pass another segment of DNA through the break before resealing it, thereby relaxing the DNA supercoiling.
  • Type IA topoisomerases typically act on negatively supercoiled DNA and are involved in DNA replication and transcription processes.
  • Examples of Type IA topoisomerases include bacterial DNA topoisomerase I and archaeal topoisomerase III.
  1. Type IB Topoisomerases:
  • Type IB topoisomerases also act on negatively supercoiled DNA but are structurally and mechanistically distinct from Type IA enzymes.
  • These enzymes cleave one strand of the DNA double helix, allowing the other strand to rotate freely around the intact phosphodiester bond.
  • Type IB topoisomerases are involved in DNA replication, transcription, and repair processes.
  • Human topoisomerase I is a well-known example of a Type IB topoisomerase, and it plays essential roles in DNA metabolism and as a target for anticancer drugs such as camptothecin derivatives.

Type IC topoisomerase refers to a hypothetical subclass of topoisomerases that may exist but have not been well-characterized or extensively studied. As of my last update in January 2022, the classification of topoisomerases typically includes Type I and Type II enzymes, further divided into subtypes IA, IB, IIA, and IIB, based on their mechanisms of action and structural features.

Type II Topoisomerases

These enzymes regulate DNA topology through the introduction of transient double-strand breaks in the DNA double helix. During cell division, these enzymes are vital for DNA replication, transcription, recombination, and chromosome segregation. Type II topoisomerases are subdivided into two subclasses: Type IIA and Type IIB.

  1. Type IIA Topoisomerases:
  • Type IIA topoisomerases cleave both strands of the DNA double helix simultaneously, generating a double-strand break.
  • They pass another segment of DNA through the break before resealing it, thereby altering DNA topology.
  • Type IIA topoisomerases are involved in DNA replication, transcription, recombination, and chromosome segregation processes.
  • Examples of Type IIA topoisomerases include bacterial DNA gyrase and eukaryotic topoisomerase II (also known as DNA topoisomerase II).
  • DNA gyrase, found in bacteria, is essential for supercoiling bacterial DNA and is a target for antibacterial drugs such as fluoroquinolones.
  1. Type IIB Topoisomerases:
  • Type IIB topoisomerases are less common and have unique structural and mechanical features than Type IIA enzymes.
  • They also cleave both strands of the DNA double helix but differ in their mode of action and regulation.
  • Examples of Type IIB topoisomerases include human topoisomerase VI.
  • Type IIB topoisomerases are less well-characterized than Type IIA enzymes, and their exact biological functions still need to be studied.

Structure of Topoisomerase

Topoisomerases are proteins with complex structures crucial for their functions in DNA metabolism. While the specific structures can vary between different types and subclasses of topoisomerases, they generally share several standard features:

  1. Catalytic Core: The catalytic core of topoisomerases contains the active site responsible for cleaving and rejoining DNA strands. This core typically consists of conserved amino acid residues that coordinate metal ions required for catalysis.
  2. DNA-binding Domains: Topoisomerases have domains or regions that specifically bind to DNA. These domains recognize and interact with the DNA substrate, facilitating the cleavage and rejoining reactions.
  3. Gate Domains: Gate domains are protein regions that undergo conformational changes to open and close the active site, allowing access to the DNA substrate. These conformational changes are essential for the catalytic cycle of topoisomerases.
  4. Linker Regions: Linker regions connect different domains of the topoisomerase protein and play a role in coordinating their movements and interactions during catalysis.
  5. Dimerization Interfaces: Many topoisomerases function as dimers, with two protein subunits coming together to form an active enzyme complex. Dimerization interfaces facilitate the formation of these complexes.
  6. Regulatory Domains: Some topoisomerases contain regulatory domains that modulate their activity in response to cellular signals or interactions with other proteins. These domains can regulate factors such as DNA binding, catalysis, and subcellular localization.
  7. Additional Structural Elements: Depending on the specific type and subclass of topoisomerase, additional structural elements may be present, such as ATP-binding domains in Type IIA topoisomerases or unique insertion domains in particular subclasses.

The structures of topoisomerases have been studied extensively using techniques like cryo-electron microscopy (cryo-EM), nuclear magnetic resonance (NMR) spectroscopy, and X-ray crystallography. 

Function of Topoisomerase

Topoisomerases play crucial roles in various cellular processes by modulating the topological state of DNA. Some of the critical roles of topoisomerases include:

  1. DNA Replication: During DNA replication, the double helix must unwind to expose the template strands for DNA polymerase. This unwinding generates positive supercoiling ahead of the replication fork. Type I topoisomerases relieve this positive supercoiling by creating transient single-strand breaks and allowing the DNA to rotate. Type II topoisomerases can also untangle DNA knots and resolve catenanes (interlinked DNA loops) that form during replication.
  2. Transcription: Transcription involves the synthesis of RNA from a DNA template. As RNA polymerase moves along the DNA strand, it generates positive supercoiling ahead and negative supercoiling behind. Topoisomerases help relieve this torsional stress by introducing transient breaks in the DNA strands.
  3. Chromosome Segregation: Chromosomes condense and segregate into daughter cells during cell division. Type II topoisomerases are particularly important for this process, as they help to resolve the interwound DNA strands (chromatids) that form during chromosome condensation. They also play a role in unlinking sister chromatids at the onset of anaphase.
  4. DNA Repair and Recombination: Topoisomerases participate in DNA repair and recombination processes by resolving DNA knots, tangles, and supercoils that can impede these processes. They facilitate the unwinding and recombination of DNA strands, promoting accurate repair of damaged DNA and genetic recombination.
  5. Regulation of Gene Expression: Topoisomerases can regulate gene expression through modulation of the accessibility of DNA to transcription factors and other regulatory proteins. By altering DNA topology, they can influence the binding of proteins to specific DNA sequences, thereby controlling gene expression levels.
  6. Response to Cellular Stress: Topoisomerases play a role in cellular responses to various stresses, including DNA damage, oxidative stress, and replication stress. They help maintain genomic stability by resolving DNA lesions and preventing the accumulation of DNA damage.

Overall, topoisomerases are essential enzymes that contribute to the maintenance of DNA structure and integrity and the regulation of various cellular processes critical for cell viability and function. Their dysregulation or inhibition can lead to genomic instability, cell death, and disease, making them important targets for therapeutic intervention.

References

  1. Nitiss, J. L., Soans, E., Rogojina, A., Seth, A., & Mishina, M. (2012). Topoisomerase assays. Current protocols in pharmacology, Chapter 3, Unit3.3–3.3.. https://doi.org/10.1002/0471141755.ph0303s57 
  2. Reece, R. J., & Maxwell, A. (1991). DNA gyrase: structure and function. Critical reviews in biochemistry and molecular biology, 26(3-4), 335–375. https://doi.org/10.3109/10409239109114072 
  3. Champoux J. J. (2001). DNA topoisomerases: structure, function, and mechanism. Annual review of biochemistry, 70, 369–413. https://doi.org/10.1146/annurev.biochem.70.1.369 

Ashma Shrestha

Hello, I am Ashma Shrestha. I had recently completed my Masters degree in Medical Microbiology. Passionate about writing and blogging. Key interest in virology and molecular biology.

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