DNA is a remarkably long molecule that must be tightly packaged within the confines of a cell. This compaction creates a challenge known as DNA topology, which refers to the geometric arrangement of the double helix in space. During essential processes like replication and transcription, the unwinding of the DNA strands creates torsional stress, causing the helix to twist upon itself, a phenomenon termed supercoiling. If this stress is not relieved, the cellular machinery responsible for copying and reading the genetic code would halt. Topoisomerases are a broad family of enzymes evolved to manage this topological stress by transiently breaking and rejoining the DNA backbone. DNA Gyrase is a specialized member of this family.
The Topoisomerase Family and Classification
Topoisomerases are present across all forms of life and are classified into two major groups based on their mechanism of action. The fundamental process involves the enzyme binding to a DNA segment, making a temporary break in the sugar-phosphate backbone, and then passing another strand through that gap before resealing the break. This mechanism allows the enzyme to alter the linking number of the DNA molecule, which measures its topological state.
Topoisomerase Type I enzymes function by creating a transient single-strand break in the DNA duplex. This nick allows the intact strand to rotate around the broken one, effectively relieving torsional stress. Type I enzymes change the linking number by increments of one and generally do not require the energy input of adenosine triphosphate (ATP) for this relaxation.
In contrast, Topoisomerase Type II enzymes operate by generating a transient double-strand break in the DNA. The enzyme passes an entire segment of the DNA helix through the gap before religating the ends. This strand-passage mechanism results in a change in the linking number by units of two. Because this mechanism requires large conformational changes, it necessitates the hydrolysis of ATP for energy.
DNA Gyrase: Structure and Unique Function
DNA Gyrase is categorized as a Type II Topoisomerase, but its structure and function set it apart from most other family members. This enzyme is predominantly found in prokaryotes, such as bacteria, and its unique activity is necessary for bacterial survival. The enzyme is structured as a heterotetramer, composed of four protein subunits: two GyrA subunits and two GyrB subunits, forming an A2B2 complex.
The GyrA subunits are responsible for DNA binding, cleavage, and rejoining of the double-stranded DNA backbone. The GyrB subunits contain the ATP-binding site and hydrolyze ATP, supplying the necessary energy for the enzyme’s function. This arrangement creates a series of gates that enable the strand-passage mechanism.
The defining characteristic of DNA Gyrase is its ability to actively introduce negative supercoils into the bacterial chromosome. Negative supercoiling is a form of underwinding that helps compact the bacterial genome and facilitates the separation of DNA strands required for replication and transcription. DNA Gyrase is the only enzyme known to actively and systematically introduce this tension.
Comparing Enzymatic Action
The primary distinction between DNA Gyrase and the broader topoisomerase family lies in the nature of the topological change they catalyze. Most Topoisomerases, including eukaryotic Type I and Type II enzymes, function primarily as “relaxers” of supercoiling. Their role is to relieve the positive supercoils, or overwinding, that build up ahead of moving replication and transcription machinery. Relaxation often requires ATP only for enzyme cycling, not for the topological change itself.
DNA Gyrase, conversely, is an “introducer” of supercoiling, specifically negative supercoiling, which is a highly energy-intensive process. This unique action maintains the overall negative supercoiled state of the bacterial genome, which is necessary for gene expression and DNA compaction.
Gyrase is also distinct from bacterial Topoisomerase IV, a related enzyme that specializes in the unlinking and separation of daughter chromosomes, a process called decatenation, at the end of replication.
The difference in energy requirements reflects their opposing roles: Relaxing Topoisomerases generally release stored torsional energy. DNA Gyrase must actively use the chemical energy from ATP hydrolysis to twist the DNA against its natural tendency. This biochemical divergence means that DNA Gyrase is actively generating the necessary genomic tension required for optimal bacterial function.
Medical Relevance as Drug Targets
The specialized functions and structural differences of these enzymes translate directly into their importance as targets for therapeutic drugs. Bacterial DNA Gyrase, along with Topoisomerase IV, is the main target for the highly successful class of antibiotics known as fluoroquinolones, such as ciprofloxacin. These drugs exploit the structural differences between the bacterial and human enzymes to achieve selective toxicity, effectively poisoning the bacterial enzyme without harming the host.
The quinolone antibiotics act by trapping the bacterial Gyrase and Topoisomerase IV in a cleaved, intermediate state, preventing the religation of the DNA strands. This leads to lethal double-strand breaks in the bacterial genome, halting replication and causing cell death. Other antibiotics, such as the coumarins, target the ATP-binding site on the GyrB subunit, inhibiting the energy supply required for the supercoiling reaction.
In human medicine, eukaryotic Topoisomerases are targeted for cancer treatment, not antibacterial action. Chemotherapy agents like camptothecins target human Topoisomerase I, while drugs such as etoposide target human Topoisomerase II. These anticancer agents operate by the same “poisoning” mechanism, trapping the host enzyme-DNA complex to induce breaks in the DNA of rapidly dividing cancer cells.