title: A microarray-based antibiotic screen identifies a regulatory role for supercoiling in the osmotic stress response of Escherichia coli.
abstract: Changes in DNA supercoiling are induced by a wide range of environmental stresses in Escherichia coli, but the physiological significance of these responses remains unclear. We now demonstrate that an increase in negative supercoiling is necessary for transcriptional activation of a large subset of osmotic stress-response genes. Using a microarray-based approach, we have characterized supercoiling-dependent gene transcription by expression profiling under conditions of high salt, in conjunction with the microbial antibiotics novobiocin, pefloxacin, and chloramphenicol. Algorithmic clustering and statistical measures for gauging cellular function show that this subset is enriched for genes critical in osmoprotectant transport/synthesis and rpoS-driven stationary phase adaptation. Transcription factor binding site analysis also supports regulation by the global stress sigma factor rpoS. In addition, these studies implicate 60 uncharacterized genes in the osmotic stress regulon, and offer evidence for a broader role for supercoiling in the control of stress-induced transcription.
authors.affiliation: Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
authors.forename: Kevin J
authors.initials: KJ
authors.lastname: Cheung
authors.forename: Vasudeo
authors.initials: V
authors.lastname: Badarinarayana
authors.forename: Douglas W
authors.initials: DW
authors.lastname: Selinger
authors.forename: Daniel
authors.initials: D
authors.lastname: Janse
authors.forename: George M
authors.initials: GM
authors.lastname: Church
mesh_terms: D000900:Anti-Bacterial Agents / Q000494:pharmacology; D001426:Bacterial Proteins / Q000235:genetics; D019610:Cytoprotection / Q000187:drug effects / Q000235:genetics; D027081:DNA Gyrase / Q000187:drug effects / Q000235:genetics; D004264:DNA Topoisomerases, Type I / Q000235:genetics / Q000378:metabolism; D004269:DNA, Bacterial / Q000235:genetics; D004278:DNA, Superhelical / Q000235:genetics / Q000502:physiology*; D004926:Escherichia coli / Q000187:drug effects / Q000235:genetics / Q000254:growth & development / Q000502:physiology*; D029968:Escherichia coli Proteins / Q000235:genetics / Q000378:metabolism; D020869:Gene Expression Profiling / Q000379:methods*; D015964:Gene Expression Regulation, Bacterial / Q000187:drug effects / Q000235:genetics / Q000502:physiology*; D016680:Genome, Bacterial; D005810:Multigene Family / Q000187:drug effects / Q000235:genetics; D009675:Novobiocin / Q000494:pharmacology; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D009997:Osmotic Pressure; D015366:Pefloxacin / Q000494:pharmacology; D011188:Potassium / Q000378:metabolism; D012808:Sigma Factor / Q000235:genetics; D012965:Sodium Chloride / Q000494:pharmacology; D013314:Stress, Mechanical; D013696:Temperature; D014158:Transcription, Genetic / Q000187:drug effects / Q000502:physiology
chemical_list: D000900:Anti-Bacterial Agents; D001426:Bacterial Proteins; D004269:DNA, Bacterial; D004278:DNA, Superhelical; D029968:Escherichia coli Proteins; D012808:Sigma Factor; C069567:sigma factor KatF protein, Bacteria; D009675:Novobiocin; D015366:Pefloxacin; D012965:Sodium Chloride; D004264:DNA Topoisomerases, Type I; D027081:DNA Gyrase; D011188:Potassium