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Genomic transcriptional response to loss of chromosomal supercoiling in Escherichia coli

Brian J Peter16, Javier Arsuaga12, Adam M Breier3, Arkady B Khodursky4, Patrick O Brown5 and Nicholas R Cozzarelli1*

Author affiliations

1 Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3204, USA

2 Mathematics Department, University of California, Berkeley, CA 94720, USA

3 Graduate Group in Biophysics, University of California, Berkeley, CA 94720, USA

4 Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, St. Paul, MN 55108, USA

5 Department of Biochemistry and Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305-5307, USA

6 Current address: Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge CB2 2QH, UK

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Citation and License

Genome Biology 2004, 5:R87  doi:10.1186/gb-2004-5-11-r87

Published: 1 November 2004



The chromosome of Escherichia coli is maintained in a negatively supercoiled state, and supercoiling levels are affected by growth phase and a variety of environmental stimuli. In turn, supercoiling influences local DNA structure and can affect gene expression. We used microarrays representing nearly the entire genome of Escherichia coli MG1655 to examine the dynamics of chromosome structure.


We measured the transcriptional response to a loss of supercoiling caused either by genetic impairment of a topoisomerase or addition of specific topoisomerase inhibitors during log-phase growth and identified genes whose changes are statistically significant. Transcription of 7% of the genome (306 genes) was rapidly and reproducibly affected by changes in the level of supercoiling; the expression of 106 genes increased upon chromosome relaxation and the expression of 200 decreased. These changes are most likely to be direct effects, as the kinetics of their induction or repression closely follow the kinetics of DNA relaxation in the cells. Unexpectedly, the genes induced by relaxation have a significantly enriched AT content in both upstream and coding regions.


The 306 supercoiling-sensitive genes are functionally diverse and widely dispersed throughout the chromosome. We propose that supercoiling acts as a second messenger that transmits information about the environment to many regulatory networks in the cell.