Researchers have uncovered the process by which DNA gyrase untangles DNA, offering new insights into this crucial biological mechanism with potential practical applications. Gyrases are important targets for treating bacterial infections, and similar human enzymes are targets for anti-cancer drugs. Understanding how gyrases function at the molecular level could lead to advancements in clinical treatments.
Imagine a classic ”landline” telephone with a coiled cord connecting the handset to the phone. The coiled telephone cord and the DN rnrnA common feature of the double helix, which holds the genetic material in every cell, is that it supercoils and tangles about itself in ways that can be hard to unravel. If this overwinding is not managed, essential processes like DNA copying and cell division can be disrupted. Fortunately, cells have a clever solution to control DNA supercoiling.
In a study published in the journal Science, researchers from Baylor College of Medicine, Université de Strasbourg, Université Paris Cité, and other collaborating institutions explain how DNA gyrase handles the supercoiling of DNA.DNA entanglements are a crucial biological mechanism that has potential applications in treating bacterial infections and anti-cancer drugs. Understanding how gyrases work at the molecular level can improve clinical treatments for these conditions. DNA supercoiling is necessary for the cell to read and make copies of genetic information, but an imbalance of supercoiling can be harmful. For instance, too little or too much supercoiling can have detrimental effects.
DNA gyrase is responsible for untangling overwound DNA, but the specifics of this process have long been unclear.
DNA minicircles and advanced imaging techniques provide insight into the first step of untangling DNA.
“Although we often think of DNA as a straight double helix, it actually exists as supercoiled loops inside cells. Studying the interactions between these supercoils and the enzymes involved in DNA functions has been difficult, so researchers usually use linear DNA models.Dr. Lynn Zechiedrich, a study author and professor at Baylor College of Medicine, stated that their laboratory has been aiming to study interactions using a DNA structure that closely resembles the coiled and looped form of DNA found in living cells. After extensive research, the Zechiedrich lab successfully developed small loops of supercoiled DNA by twisting the traditional linear DNA double helix.The researchers previously studied the 3-D structures of supercoiled minicircles and found that they form a variety of shapes. They believed that enzymes like gyrase would recognize these shapes. In their recent study, the researchers used electron cryomicroscopy and other advanced imaging techniques to confirm their hypothesis about the interactions of DNA gyrase with DNA minicircles.s.
Dr. Valérie Lamour, an associate professor at the Institut de Génétique et de Biologie Moléculaire et Cellulaire, Université de Strasbourg, stated that her lab has been focusing on the study of DNA gyrases, which are large enzymes responsible for regulating DNA supercoiling. She explained that supercoiling is important for confining about 2 meters (6.6 feet) of linear DNA into the small nucleus of the cell.
Inside the nucleus, the DNA supercoils, twisting and folding into various shapes. It’s like trying to fit a long piece of string into a small box.Twisting the telephone cord multiple times on itself mentioned at the beginning will cause it to overwind and create a loop by crossing over DNA chains, tightening the structure.
“We found, as we had predicted, that gyrase is drawn to the supercoiled minicircle and positions itself inside this supercoiled loop,” said Dr. Jonathan Fogg, a co-author and senior staff scientist of molecular virology and microbiology, and biochemistry and molecular pharmacology in the Zechiedrich lab.
“This is the initial step of the mechanism that triggers the enzyme to resolve DNA entanglements,” Lamour explained.
“DNA gyrase, now surrounded by the supercoiled loop, is prompted to initiate the process of untangling DNA,” clarified Dr. Lamour.by a tightly supercoiled loop, one DNA helix will be cut in the loop, the other DNA helix will be passed through the cut, and then the break will be resealed. This process relaxes the overwinding and eases tangles, which regulates DNA supercoiling and controls DNA activity,” Zechiedrich explained. “It’s like watching a rodeo. Just like roping cattle with a lasso, supercoiled looped DNA captures gyrase in the first step. Gyrase then cuts one double-helix of the DNA lasso and passes the other helix through the break to get free.”
Dr. Marc Nadal, a professor at the École Normale in Paris and co-corresponding author, confirmed the observation of the path of the DNA wrapped in the loop.The loop around gyrase is observed using magnetic tweezers, a technique that measures the deformation and fluctuations in the length of a single DNA molecule. This allows for information that is typically hidden when looking at multiple molecules in traditional experiments. Interestingly, the “DNA strand inversion model” for gyrase activity was proposed in 1979 by Drs. Patrick O. Brown and the late Nicholas R. Cozzarelli, also in a Science paper, before researchers had access to supercoiled minicircles or the 3-D molecular structure of the enzyme.”It is especially significant to me that 45 years later, we are finally able to provide experimental evidence that supports their hypothesis because Nick was my postdoctoral mentor,” Zechiedrich said.
“This research opens up numerous possibilities for studying the mechanism of this conserved class of enzymes, which have significant clinical importance,” Lamour said.
“This study promotes new concepts about how DNA activities are controlled. We suggest that DNA is not just a passive biomolecule influenced by enzymes, but an active one that utilizes supercoiling, looping, and 3-D shapes to control the accessibility of enzymes like gyrase to specific DNA sequences in a variety of circumstances.Fogg stated that this discovery is likely to have an impact on how cells respond to antibiotics and other treatments.