DNA, or deoxyribonucleic acid, is the fundamental blueprint that guides the growth, development, functioning, and reproduction of all living organisms. This molecule contains the complete set of genetic instructions, dictating characteristics and processes within a cell. DNA is highly compact within a cell, and its precise management is crucial for an organism’s survival.
The Challenge of DNA Supercoiling
The long, double-helix DNA molecule must be tightly packed to fit within the confined spaces of a cell, such as a bacterial cell or a eukaryotic nucleus. For example, the approximately two meters of DNA in a human cell must fit into a nucleus merely micrometers in diameter. This extensive packaging involves DNA coiling around various proteins, forming highly condensed structures.
DNA replication and transcription require unwinding the double helix to access genetic information. This unwinding introduces torsional stress, similar to twisting a rubber band. As enzymes move along DNA, positive supercoils, or overwound regions, accumulate ahead of them. These accumulating twists can impede or even halt biological functions if not properly managed. Cells also require the introduction of negative supercoils, or underwound regions, to facilitate DNA compaction and initiate these processes.
DNA Gyrase: The Essential Unwinding Enzyme
Cells use specialized enzymes called topoisomerases to manage DNA coiling. DNA gyrase is a type II topoisomerase, playing a central role in managing DNA topology within bacteria. Its primary function is to introduce negative supercoils into DNA, which helps compact the bacterial chromosome and alleviate torsional strain.
DNA gyrase also relaxes positive supercoils that accumulate during DNA replication and transcription. This dual ability ensures DNA remains accessible for these processes while maintaining its compact structure. The enzyme’s precise control over DNA supercoiling is critical for accurate bacterial genome replication, gene expression, and DNA repair mechanisms. These functions make DNA gyrase essential for bacterial survival.
How DNA Gyrase Works
DNA gyrase operates as a tetrameric enzyme, composed of two GyrA subunits and two GyrB subunits, forming a symmetrical structure. It uses a “two-gate mechanism” to alter DNA topology. The enzyme first binds to a DNA segment, referred to as the “G-segment,” that will be cleaved.
After binding, DNA gyrase temporarily creates a double-strand break in the G-segment. A second DNA segment, known as the “T-segment,” is then captured and passed through this break. This strand passage is an energy-dependent process, powered by the binding and hydrolysis of adenosine triphosphate (ATP) molecules. Two ATP molecules are hydrolyzed per complete catalytic cycle.
ATP binding to GyrB subunits causes a conformational change, closing the “N-gate” and trapping the T-segment. The GyrA subunits cleave and reseal the G-segment. Once the T-segment passes through, the G-segment break is resealed, and the N-gate reopens upon ATP hydrolysis, resetting the enzyme. Each complete cycle results in the introduction of two negative supercoils into the DNA.
DNA Gyrase as a Medical Target
DNA gyrase’s critical role in bacterial survival, coupled with its structural differences from human topoisomerases, makes it an effective target for antibiotic development. Targeting this enzyme allows for selective disruption of bacterial processes while minimizing adverse effects on human cells. Several classes of antibiotics have been developed to inhibit DNA gyrase to combat bacterial infections.
Quinolones, including drugs like ciprofloxacin and nalidixic acid, represent a major class of antibiotics that target DNA gyrase. These drugs bind to the DNA-gyrase complex, trapping the enzyme on the DNA after it has made a double-strand break but before it can reseal it. This stabilization leads to an accumulation of lethal double-stranded DNA breaks, causing bacterial cell death.
Another class of antibiotics, the aminocoumarins, exemplified by novobiocin, inhibits DNA gyrase through a different mechanism. Instead of stabilizing the DNA-enzyme complex, aminocoumarins interfere with the ATP hydrolysis activity of the enzyme. By blocking this energy-providing step, these antibiotics prevent DNA gyrase from performing its supercoiling function. The disruption of DNA synthesis and maintenance through these mechanisms makes DNA gyrase inhibitors effective treatments for a range of bacterial infections, including those affecting the urinary tract, respiratory system, and gastrointestinal tract.