Structure, function, and evolution of topoisomerase modulatory proteins in bacteria

SUMMARYDNA topoisomerases are essential for maintaining the integrity and functionality of the genome. By homeostatically controlling the genome topology in bacteria, these enzymes influence essential cellular processes such as gene expression, replication, recombination, and chromosome segregation. Although DNA topoisomerases were initially considered to act as stand-alone enzymes, they are now being recognized as integral components of dynamic protein complexes that perform diverse functions in vivo. The discovery of several proteinaceous modulators of DNA topoisomerases has expanded the understanding of their functional versatility. These are encoded either by the bacterial chromosome or extrachromosomal elements like plasmids and bacteriophages. Chromosomally encoded modulators are engaged in fine-tuning topoisomerase activity, enabling them to carry out specialized cellular functions beyond their canonical enzymatic roles. Crucially, they prevent genomic instability that may arise from dysregulated topoisomerase activity. By altering DNA topology, modulatory proteins can influence transcriptional bursting, leading to epigenetic heterogeneity within the bacterial populations, crucial for bacterial stress adaptation. In contrast, topoisomerase interacting proteins encoded by plasmids and phages have dedicated roles in facilitating plasmid maintenance and phage propagation by suppressing host defenses and promoting horizontal gene transfer. We present a comprehensive analysis of the topoisomerase modulatory proteins discovered so far, offering insights into the mechanisms by which DNA topology and homeostasis are maintained within the intracellular environment. We project the potential of topoisomerase modulator-based drug design as a promising strategy for combating multidrug-resistant bacterial pathogens.