title: An increase in negative supercoiling in bacteria reveals topology-reacting gene clusters and a homeostatic response mediated by the DNA topoisomerase I gene.
abstract: We studied the transcriptional response to an increase in DNA supercoiling in Streptococcus pneumoniae by using seconeolitsine, a new topoisomerase I inhibitor. A homeostatic response allowing recovery of supercoiling was observed in cells treated with subinhibitory seconeolitsine concentrations. Supercoiling increases of 40.7% (6 μM) and 72.9% (8 μM) were lowered to 8.5% and 44.1%, respectively. Likewise, drug removal facilitated the recovery of cell viability and DNA-supercoiling. Transcription of topoisomerase I depended on the supercoiling level. Also specific binding of topoisomerase I to the gyrase A gene promoter was detected by chromatin-immunoprecipitation. The transcriptomic response to 8 μM seconeolitsine had two stages. An early stage, associated to an increase in supercoiling, affected 10% of the genome. A late stage, manifested by supercoiling recovery, affected 2% of the genome. Nearly 25% of the early responsive genes formed 12 clusters with a coordinated transcription. Clusters were 6.7-31.4 kb in length and included 9-22 responsive genes. These clusters partially overlapped with those observed under DNA relaxation, suggesting that bacteria manage supercoiling stress using pathways with common components. This is the first report of a coordinated global transcriptomic response that is triggered by an increase in DNA supercoiling in bacteria.
authors.affiliation: Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain.
authors.forename: María-José
authors.initials: MJ
authors.lastname: Ferrándiz
authors.affiliation: Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain.
authors.forename: Antonio J
authors.initials: AJ
authors.lastname: Martín-Galiano
authors.affiliation: Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain.
authors.forename: Cristina
authors.initials: C
authors.lastname: Arnanz
authors.affiliation: Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain.
authors.forename: Isabel
authors.initials: I
authors.lastname: Camacho-Soguero
authors.affiliation: Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain.
authors.forename: José-Manuel
authors.initials: JM
authors.lastname: Tirado-Vélez
authors.affiliation: Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain Presidencia. Consejo Superior de Investigaciones Científicas, 28006 Madrid, Spain agcampa@isciii.es.
authors.forename: Adela G
authors.initials: AG
authors.lastname: de la Campa
mesh_terms: D052117:Benzodioxoles / Q000494:pharmacology; D027081:DNA Gyrase / Q000235:genetics; D004264:DNA Topoisomerases, Type I / Q000096:biosynthesis / Q000235:genetics* / Q000378:metabolism; D004269:DNA, Bacterial / Q000187:drug effects / Q000235:genetics; D004278:DNA, Superhelical / Q000187:drug effects / Q000235:genetics*; D015964:Gene Expression Regulation, Bacterial / Q000187:drug effects; D005798:Genes, Bacterial / Q000235:genetics; D006706:Homeostasis / Q000187:drug effects / Q000235:genetics*; D050296:Microbial Viability / Q000187:drug effects / Q000235:genetics; D005810:Multigene Family; D010616:Phenanthrenes / Q000494:pharmacology; D013296:Streptococcus pneumoniae / Q000187:drug effects / Q000235:genetics*; D014158:Transcription, Genetic / Q000187:drug effects; D059467:Transcriptome / Q000187:drug effects / Q000235:genetics
chemical_list: D052117:Benzodioxoles; D004269:DNA, Bacterial; D004278:DNA, Superhelical; D010616:Phenanthrenes; C000620217:seconeolitsine; D004264:DNA Topoisomerases, Type I; D027081:DNA Gyrase