DNA gyrase cleavage sites distribution across the Streptococcus pneumoniae genome
To determine the genome-wide location of gyrase, we mapped its cleavage sites in the Streptococcus pneumoniae genome by using the fluoroquinolones levofloxacin or moxifloxacin. We used a CHIP-Seq-based method to localize gyrase cleavage sites (GCSs) with single nucleotide resolution. For immunoprecipitation of gyrase we used a strain carrying the GyrA-3-Flag tag and anti-Flag antibodies. Duplicate experiments were performed for both drugs, and 1,517 GCSs common to all treatments were considered for further analysis. Of these, the majority (92.7%, 1,406) were located within protein-coding genes and were associated with high transcription. GATC was the most common sequence cleaved by gyrase, accounting for 1,406 GCSs, were located within protein-coding genes and associated with high transcription. Gyrase was more active on highly expressed genes, as determined by RNA-Seq, compared to low expressed genes. Reagarding the transcriptional topological domains, the two most transcribed DOWN and pcNRs domains showed the highest frequency of GCSs, while the least transcribed AT-rich domains showed the lowest frequency. The same 4-base GCS motif, GnnC, was identified regardless of the drug used. GATC was the most frequently cleaved sequence by gyrase, accounting for 21.2 % of all GCSs. We obtained evidence that methylation at GATC by DpnII or DpnIII methylases interferes with gyrase cleavage. These results are discussed in the context of the evolution of fluoroquinolone resistance in S. pneumoniae.