The unbalance between the enzymes that compact DNA cause bacterial death

Supercoiling is the phenomenon by which DNA molecules twist upon themselves, resulting in different levels of torsional stress and compaction. Supercoiling allows bacteria to efficiently package their DNA into a compact space within the cell, enabling them to fit a large amount of genetic material into a small cellular compartment. It plays a crucial role in various DNA processes, such as replication, transcription, recombination, repair, and segregation, and it affects gene expression and virulence in many bacteria. There are two types of supercoiling: positive supercoiling and negative supercoiling. Positive supercoiling occurs when the DNA is over-twisted, resulting in a tighter and more compact structure. Negative supercoiling, on the other hand, involves the DNA being under-twisted, resulting in a looser structure. Supercoiling is regulated by the balance between two enzymes: gyrase and topoisomerase I (TopoI), which introduce negative and positive supercoils, respectively.  Supercoiling is an attractive target for antibiotics. Some antibiotics, such as fluoroquinolones, work by inhibiting the activity of DNA gyrase, an enzyme that helps introduce negative supercoiling in bacterial DNA. By interfering with DNA gyrase, these antibiotics disrupt the normal supercoiling dynamics, leading to DNA damage and inhibition of bacterial growth. The balance between gyrase and TopoI activities is influenced by environmental factors and antibiotic stress. However, the exact relationship between gyrase and TopoI activities and supercoiling levels in bacteria is not well understood.

In a new study published in the peer-reviewed journal Frontiers in Microbiology¸ Spanish researchers: PhD candidate Míriam García-López, Dr. Diego Megias, Dr. María-José Ferrándiz and led by Professor Adela G. de la Campa from Instituto de Salud Carlos III and Consejo Superior de Investigaciones Científicas investigated how the balance between two enzymes, gyrase and topoisomerase I, affects the supercoiling, nucleoid compaction, and viability of the human pathogen Streptococcus pneumoniae. They measured the levels of supercoiling and nucleoid compaction under different conditions of gyrase and topoisomerase I activities, and evaluated the impact of these factors on bacterial growth and survival.

The research team findings showed a good correlation between supercoiling density (σ) measured by 2D-agarose gel electrophoresis and nucleoid compaction measured by super-resolution confocal microscopy, suggesting that these methods can be used interchangeably to estimate supercoiling levels in bacteria. They explained that their results also showed that the gyrase:TopoI enzymes proportion determines the optimal level of supercoiling for bacterial viability, and that deviations from this proportion can cause hyper-supercoiling and lethality. They noted that their results were consistent with previous studies in other types of bacteria, such as Escherichia coli and Bacillus subtilis, which also showed that altering the balance between gyrase and TopoI activities affects supercoiling and growth. The authors speculated that the optimal gyrase:TopoI enzymes proportion might vary depending on the bacterial species, genome size and structure, growth phase, and environmental conditions. They proposed that the equilibrium between gyrase and TopoI activities might be a mechanism to modulate supercoiling in response to different stimuli, such as nutrient availability, pH, temperature, oxidative stress, or antibiotic exposure. They remarked that their results also shed new light on the mechanism of action of topoisomerase-targeting antibiotics, such as novobiocin, or levofloxacin, which inhibit gyrase activity and induce hyper-supercoiling and DNA damage. According to the authors, their findings will have implications for the development of new strategies to combat antibiotic resistance, such as using combination therapies that target both gyrase and TopoI activities to enhance the efficacy of existing antibiotics or to overcome resistance mechanisms. They also expressed interest in exploring the role of other topoisomerases, such as topoisomerase IV, in supercoiling regulation and bacterial physiology.

Understanding supercoiling and its importance in bacteria treatments can help researchers develop strategies to selectively target bacterial DNA and disrupt crucial cellular processes. This knowledge contributes to the development of new antibiotics and therapeutic interventions against bacterial infections. Professor Adela G. de la Campa and her colleagues revealed the important role of the balance between gyrase and TopoI activities in regulating supercoiling, nucleoid compaction, and viability in S. pneumoniae. The authors demonstrated that the optimal gyrase:TopoI enzymes proportion is essential for maintaining normal supercoiling and growth, and that deviations from this proportion can cause hyper-supercoiling and lethality. The study also provided new insights into the mechanism of action of topoisomerase-targeting antibiotics and suggested potential strategies to combat antibiotic resistance by targeting both gyrase and TopoI activities.