ExpressDB Yeast Expression Dataset 55 Description (original) (raw)

Information Item

Value

Dataset Name

Affymetrix chips for pefloxacin induction

Dataset Number

Short Description

Affymetrix Expression Experiments showing effect of induction by pefloxacin.

Source URL

http://arep.med.harvard.edu/supercoiling/supplement.htm

Reference

Cheung, KJ, Badarinarayana,V, Selinger, D, Janse, D, and Church, GM (2002)A microarray-based antibiotic screen identifies a regulatory role for supercoiling in the osmotic stress response of Escherichia coli. Genome Research Feb;13(2):206-15.

Strains

NONE

Conditions

Contains replicates of two samples: 0 timepoint and 7 minutes
post induction with pefloxacin, plus a single sample 1 minute post induction with pefloxacin.

Date Added to ExpressDB

Aug 10 2001 10:49:34:236AM

Number of Measures on ExpressDB

60 (here to download dataset and view measure details)

Long Description

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.
Data Set loaded by Wayne

Please contact Wayne Rindone for more information, or with any questions, comments, or concerns.