title: Hot-spot consensus of fluoroquinolone-mediated DNA cleavage by Gram-negative and Gram-positive type II DNA topoisomerases.
abstract: Bacterial DNA gyrase and topoisomerase IV are selective targets of fluoroquinolones. Topoisomerase IV versus gyrase and Gram-positive versus Gram-negative behavior was studied based on the different recognition of DNA sequences by topoisomerase-quinolone complexes. A careful statistical analysis of preferred bases was performed on a large number (>400) of cleavage sites. We found discrete preferred sequences that were similar when using different enzymes (i.e. gyrase and topoisomerase IV) from the same bacterial source, but in part diverse when employing enzymes from different origins (i.e. Escherichia coli and Streptococcus pneumoniae). Subsequent analysis on the wild-type and mutated consensus sequences showed that: (i) Gn/Cn-rich sequences at and around the cleavage site are hot spots for quinolone-mediated strand breaks, especially for E. coli topoisomerases: we elucidated positions required for quinolone and enzyme recognition; (ii) for S. pneumoniae enzymes only, A and T at positions -2 and +6 are discriminating cleavage determinants; (iii) symmetry of the target sequence is a key trait to promote cleavage and (iv) the consensus sequence adopts a heteronomous A/B conformation, which may trigger DNA processing by the enzyme-drug complex.
authors.affiliation: Department of Pharmaceutical Sciences, University of Padova, 35131 Padova, Italy.
authors.forename: Sara N
authors.initials: SN
authors.lastname: Richter
authors.forename: Giulia
authors.initials: G
authors.lastname: Giaretta
authors.forename: Valentina
authors.initials: V
authors.lastname: Comuzzi
authors.forename: Elisabetta
authors.initials: E
authors.lastname: Leo
authors.forename: Lesley A
authors.initials: LA
authors.lastname: Mitchenall
authors.forename: L Mark
authors.initials: LM
authors.lastname: Fisher
authors.forename: Anthony
authors.initials: A
authors.lastname: Maxwell
authors.forename: Manlio
authors.initials: M
authors.lastname: Palumbo
mesh_terms: D000900:Anti-Bacterial Agents / Q000737:chemistry*; D001483:Base Sequence; D002939:Ciprofloxacin / Q000737:chemistry*; D016384:Consensus Sequence; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D027081:DNA Gyrase / Q000737:chemistry* / Q000378:metabolism; D027101:DNA Topoisomerase IV / Q000737:chemistry* / Q000378:metabolism; D004926:Escherichia coli / Q000201:enzymology*; D024841:Fluoroquinolones / Q000737:chemistry*; D000077735:Gemifloxacin; D006147:Guanine / Q000737:chemistry; D009287:Naphthyridines / Q000737:chemistry*; D013296:Streptococcus pneumoniae / Q000201:enzymology*; D013379:Substrate Specificity
chemical_list: D000900:Anti-Bacterial Agents; D024841:Fluoroquinolones; D009287:Naphthyridines; D002939:Ciprofloxacin; D006147:Guanine; D004247:DNA; D027101:DNA Topoisomerase IV; D027081:DNA Gyrase; D000077735:Gemifloxacin