Genomic transcriptional response to loss of chromosomal supercoiling in Escherichia coli

Brian J Peter¹^,6 , Javier Arsuaga¹^,2, Adam M Breier³, Arkady B Khodursky⁴, Patrick O Brown⁵ and Nicholas R Cozzarelli¹

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

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

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

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

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

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

author email corresponding author email

Genome Biology 2004, 5:R87doi:10.1186/gb-2004-5-11-r87


Published:	1 November 2004

Subject areas: Microbiology and parasitology, Molecular biology, Genome studies, Genetics

Abstract

Background

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.

Results

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.

Conclusions

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.