Gyrase is a specialized enzyme belonging to a class known as topoisomerases, which are responsible for managing the intricate structure of DNA within living cells. It is particularly recognized for its role in controlling DNA topology, specifically by introducing negative supercoils. This enzyme’s function is fundamental for the proper operation of many biological processes, ensuring the genetic material remains accessible and organized. Without gyrase, the stability and function of DNA would be compromised, highlighting its significance in all organisms.
The Problem of DNA Supercoiling
DNA, a long and tightly packed molecule, faces a constant challenge known as supercoiling during essential cellular activities. When the DNA double helix unwinds for processes like replication or transcription, it creates torsional stress, similar to twisting a rubber band. This stress can manifest as positive supercoils, where the DNA becomes overwound and more compact, or negative supercoils, where it becomes underwound and less compact, forming loops.
Uncontrolled accumulation of positive supercoils ahead of moving enzymes, such as RNA polymerase or DNA polymerase, can impede their progression. If this tension is not relieved, it can halt processes like DNA replication and transcription. Cells therefore require mechanisms to manage these topological changes, ensuring the DNA remains in a state that allows its strands to separate and recombine.
Gyrase’s Mechanism of Action
Gyrase introduces negative supercoils into DNA, a process that requires energy from ATP hydrolysis. The enzyme first binds to a segment of DNA, often referred to as the “gate” or G-segment, and wraps approximately 130 base pairs of DNA around itself in a positive superhelical sense.
Following DNA binding, gyrase creates a transient double-strand break in the G-segment, forming a “DNA gate.” Simultaneously, another segment of DNA, known as the “transported” or T-segment, is captured by the enzyme’s N-terminal domains, which form a protein clamp that closes upon ATP binding. The T-segment is then passed through the transient break in the G-segment, a step accompanied by the hydrolysis of the first ATP molecule.
After the T-segment has passed through, gyrase rejoins the broken strands of the G-segment, effectively changing the linking number of the DNA by two in each enzymatic cycle. The hydrolysis of a second ATP molecule then returns the enzyme to its initial state. This unique ability to introduce negative supercoils is what distinguishes gyrase from other type II topoisomerases, which primarily relax supercoils.
Gyrase’s Role in Cellular Processes
Gyrase maintains genome stability and facilitates cellular processes. During DNA replication, as the double helix unwinds at the replication fork, positive supercoils accumulate ahead of the moving polymerase. Gyrase relieves this torsional stress by introducing negative supercoils, allowing the replication fork to proceed and ensuring accurate DNA duplication.
In gene transcription, the unwinding of DNA by RNA polymerase also generates torsional stress. Gyrase helps to relax the positive supercoils that build up in front of the transcription complex, enabling gene expression. Beyond replication and transcription, gyrase also contributes to DNA repair and recombination processes by regulating DNA topology.
Gyrase as a Drug Target
Bacterial DNA gyrase is a target for antibiotic development due to its distinct structure and function compared to human topoisomerases. Since gyrase is absent in higher eukaryotes and is an enzyme required for bacterial survival, inhibiting its activity can lead to bacterial cell death. This difference allows for the design of drugs that selectively target bacterial enzymes without harming human cells.
Fluoroquinolones, a widely used class of antibiotics, act by inhibiting bacterial gyrase. Examples include ciprofloxacin and levofloxacin. These drugs interfere with the enzyme’s ability to reseal the DNA strands after cleavage, leading to the accumulation of double-strand breaks in the bacterial DNA. This damage prevents DNA replication and repair, causing bacterial cell death.
Despite their effectiveness, the widespread use of fluoroquinolones has led to the emergence of antibiotic resistance, often through mutations in the gyrase enzyme itself. These mutations, frequently occurring in specific regions of the gyrA and gyrB genes, can reduce the drug’s binding affinity or alter the enzyme’s catalytic activity, making the bacteria less susceptible to the antibiotic. Ongoing research aims to develop new gyrase inhibitors that can overcome these resistance mechanisms.