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Journal of Bacteriology, February 2008, p. 1084-1096, Vol. 190, No. 3
0021-9193/08/$08.00+0     doi:10.1128/JB.01092-07
Copyright © 2008, American Society for Microbiology. All Rights Reserved.

Transcription Profiling of the Stringent Response in Escherichia coli ^,

Tim Durfee,^1* Anne-Marie Hansen,^2, Huijun Zhi,^2, Frederick R. Blattner,¹ and Ding Jun Jin^2*

Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706,¹ Transcription Control Section, Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute-Frederick, National Institutes of Health, Frederick, Maryland 21702²

Received 11 July 2007/ Accepted 14 November 2007

The bacterial stringent response serves as a paradigm for understanding global regulatory processes. It can be triggered by nutrient downshifts or starvation and is characterized by a rapid RelA-dependent increase in the alarmone (p)ppGpp. One hallmark of the response is the switch from maximum-growth-promoting to biosynthesis-related gene expression. However, the global transcription patterns accompanying the stringent response in Escherichia coli have not been analyzed comprehensively. Here, we present a time series of gene expression profiles for two serine hydroxymate-treated cultures: (i) MG1655, a wild-type E. coli K-12 strain, and (ii) an isogenic relA251 derivative defective in the stringent response. The stringent response in MG1655 develops in a hierarchical manner, ultimately involving almost 500 differentially expressed genes, while the relA251 mutant response is both delayed and limited in scope. We show that in addition to the down-regulation of stable RNA-encoding genes, flagellar and chemotaxis gene expression is also under stringent control. Reduced transcription of these systems, as well as metabolic and transporter-encoding genes, constitutes much of the down-regulated expression pattern. Conversely, a significantly larger number of genes are up-regulated. Under the conditions used, induction of amino acid biosynthetic genes is limited to the leader sequences of attenuator-regulated operons. Instead, up-regulated genes with known functions, including both regulators (e.g., rpoE, rpoH, and rpoS) and effectors, are largely involved in stress responses. However, one-half of the up-regulated genes have unknown functions. How these results are correlated with the various effects of (p)ppGpp (in particular, RNA polymerase redistribution) is discussed.

Published ahead of print on 26 November 2007.

Supplemental material for this article may be found at http://jb.asm.org/.

Present address: Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201.

Present address: Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814.

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