Transcriptional consequences of DNA gyrase inhibition

DNA gyrase is an essential enzyme whose activity is required for DNA replication and chromosome maintenance. Inhibition of gyrase results in multiple physiological effects including changes in DNA superhelicity, replication arrest and DNA damage. Using genetic, genomic, statistical and biochemical techniques, we have untangled the contribution of individual effects, assessed their relative significance and concluded that: i) DNA replication is required for the formation of spatial transcriptional domains; ii) transcriptional response to gyrase inhibition is coordinated between at least two modules involved in DNA maintenance, relaxation and damage response; iii) genes whose transcriptional response to gyrase inhibition does not depend on the activity of topoisomerase I can be classified on the basis of the GC excess in their upstream and coding sequences into, respectively, activated and repressed by gyrase inhibition; iv) relaxation by topoisomerase I dominates the transcriptional response upon gyrase inhibition, followed by the effects of replication and RecA. Keywords: time course Isogenic mutants (recA-, topA- and dnaC(Ts)) are deficient in one of cellular processes upon gyrase inhibition: DNA repair, DNA relaxation and DNA replication. With time course (0, 5, 10, 15 and 20 min) treatment of gyrase inhibitor, transcriptional responses are dissected in terms of three celluar processes. Reference samples are collected from non-treated cells at 0 min.