Distribution of gyrase and topoisomerase IV on bacterial nucleoid: implications for nucleoid organization

We explored the existence of nucleoid DNA loops in Escherichia coli by studying the distribution of bacterial type II topoisomerases (Topo IIs). Norfloxacin-induced high molecular weight (HMW) DNA fragmentation of nucleoid, an event reminiscent of the excision of eukaryotic chromosomal DNA loops mediated by topoisomerase II (TOP2). The size of the HMW DNA fragments induced by norfloxacin was affected by transcription, translation and growth phases of bacteria. The involvement of bacterial Topo IIs in the generation of these HMW DNA fragments is supported by the following observations: (i) the excised loop-sized DNA fragments were covalently linked to proteins; (ii) the norfloxacin-induced excision of DNA loops was highly reversible; (iii) coumermycin A1 antagonized the excision of DNA loops induced by norfloxacin; (iv) this antagonistic effect was reduced in either gyrase or topo IV mutants conferring coumarin resistance and (v) norfloxacin-induced reversible, gyrase-mediated DNA cleavage in vitro. Importantly, studies on coumarin- and/or quinolone-resistant mutant strains showed that DNA gyrase, rather than topoisomerase IV, plays the major role in the generation of loop-sized HMW DNA fragments. In sum, our study suggests a potential role of Topo IIs in the arrangement of DNA supercoiling loop domains in prokaryotic cells.