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Genomic transcriptional response to loss of chrosomal supercoiling in E.coli

Genomic transcriptional response to loss of chrosomal supercoiling in E.coli

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Genome Biology 2004, 5: R87 comment reviews reports deposited research refereed research interactions information Open Access 2004 Peter et al. Volume 5, Issue 11, Article R87 Research Genomic transcriptional response to loss of chromosomal supercoiling in Escherichia coli Brian J Peter , Javier Arsuaga *† , Adam M Breier , Arkady B Khodursky § , Patrick O Brown and Nicholas R Cozzarelli * Addresses: * Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3204, USA. Mathematics Department, University of California, Berkeley, CA 94720, USA. Graduate Group in Biophysics, University of California, Berkeley, CA 94720, USA. § Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, St. Paul, MN 55108, USA. Department of Biochemistry and Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305-5307, USA. ¥ Current address: Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge CB2 2QH, UK. Correspondence: Nicholas R Cozzarelli. E-mail: [email protected] © 2004 Peter et al .; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Transcriptional response to supercoiling in bacteria <p>Microarray analysis shows that transcription of 306 E. Coli genes is affected by changes in the level of chromosome supercoiling, sug- gesting that supercoiling transmits regulatory signals from the environment to many cellular pathways.</p> 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.
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