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J. Biol. Chem., Vol. 282, Issue 15, 11230-11237, April 13, 2007

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Transition of Escherichia coli from Aerobic to Micro-aerobic Conditions Involves Fast and Slow Reacting Regulatory Components^*

Jonathan D. Partridge, Guido Sanguinetti, David P. Dibden, Ruth E. Roberts, Robert K. Poole, and Jeffrey Green¹

From the Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield S10 2TN, United Kingdom and the Department of Computer Science, The University of Sheffield, Sheffield S1 4DP, United Kingdom

Understanding life at a systems level is a major aim of biology. The bacterium Escherichia coli offers one of the best opportunities to achieve this goal. It is a metabolically versatile bacterium able to respond to changes in oxygen availability. This ability is a crucial component of its lifestyle, allowing it to thrive in aerobic external environments and under the oxygen-starved conditions of a host gut. The controlled growth conditions of chemostat culture were combined with transcript profiling to investigate transcriptome dynamics during the transition from aerobic to micro-aerobic conditions. In addition to predictable changes in transcripts encoding proteins of central metabolism, the abundances of transcripts involved in homeostasis of redox-reactive metals (Cu and Fe), and cell envelope stress were significantly altered. To gain further insight into the responses of the regulatory networks, the activities of key transcription factors during the transition to micro-aerobic conditions were inferred using a probabilistic modeling approach, which revealed that the response of the direct oxygen sensor FNR was rapid and overshot, whereas the indirect oxygen sensor ArcA reacted more slowly. Similarly, the cell envelope stress sensors RpoE and CpxR reacted rapidly and more slowly, respectively. Thus, it is suggested that combining rapid and slow reacting components in regulatory networks might be a feature of systems in which a signal is perceived by two or more functionally related transcription factors controlling overlapping regulons.

Received for publication, January 25, 2007 , and in revised form, February 15, 2007.

^* This work was supported by a grant from the United Kingdom Biotechnology and Biological Sciences Research Council. The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

The on-line version of this article (available at http://www.jbc.org) contains supplemental Tables S1-S3, Fig. S1, and methods.

¹ To whom correspondence should be addressed: Dept. of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield S10 2TN, UK. Tel.: 44-114-222-4403; Fax: 44-114-222-2800; E-mail: jeff.green{at}sheffield.ac.uk.

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