Supplementary material

Last updated: September 6, 2002



A microarray-based antibiotic screen identifies a regulatory role for supercoiling in the osmotic stress response of Escherichia coli


Kevin J. Cheung, Vasudeo Badarinarayana, Douglas Selinger, Daniel Janse, and George M. Church






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 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.







  1. Clusters 0-5 (full listing of genes sorted by cluster with scores based on the supercoiling-dependency metric)
  2. Table 3 (detailed)
  3. Raw Affymetrix datasets can be found here.
  4. Software
    1. Catscore package: perl scripts for testing within-cluster statistical enrichment for cellular function (see readme)
    2. Draw_clusters.m: Matlab script for generating figures from GeneCluster output




Copyright (c) 2002 by Kevin Cheung and the President and Fellows of Harvard University