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Originally published In Press as doi:10.1074/jbc.M209268200 on November 5, 2002

J. Biol. Chem., Vol. 278, Issue 3, 1494-1503, January 17, 2003
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The Role of the Alarmone (p)ppGpp in sigma N Competition for Core RNA Polymerase*

Andrew D. LaurieDagger §, Lisandro M. D. BernardoDagger , Chun Chau SzeDagger , Eleonore SkärfstadDagger , Agnieszka Szalewska-PalaszDagger , Thomas Nyström||, and Victoria ShinglerDagger **

From the Dagger  Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden and the || Department of Cell and Molecular Biology-Microbiology, Göteborg University, Box 462, 405 30 Göteborg, Sweden

Some promoters, including the DmpR-controlled sigma N-dependent Po promoter, are effectively rendered silent in cells lacking the nutritional alarmone (p)ppGpp. Here we demonstrate that four mutations within the housekeeping sigma D-factor can restore sigma N-dependent Po transcription in the absence of (p)ppGpp. Using both in vitro and in vivo transcription competition assays, we show that all the four sigma D mutant proteins are defective in their ability to compete with sigma N for available core RNA polymerase and that the magnitude of the defect reflects the hierarchy of restoration of transcription from Po in (p)ppGpp-deficient cells. Consistently, underproduction of sigma D or overproduction of the anti-sigma D protein Rsd were also found to allow (p)ppGpp-independent transcription from the sigma N-Po promoter. Together with data from the direct effects of (p)ppGpp on sigma N-dependent Po transcription and sigma -factor competition, the results support a model in which (p)ppGpp serves as a master global regulator of transcription by differentially modulating alternative sigma -factor competition to adapt to changing cellular nutritional demands.

* This work was supported by grants from the Swedish Research Councils for Natural Sciences and the Swedish Foundation for Strategic Research.The costs of publication of this article were defrayed in part by the payment of page charges. The article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

§ Current address: Landcare Research, P. O. Box 69, Lincoln 8152, New Zealand.

Current address: Dept. of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan.

** To whom correspondence should be addressed. Tel.: 46-90-785-2534; Fax: 46-90-771420; E-mail victoria.shingler@molbiol.umu.se.

Copyright © 2003 by The American Society for Biochemistry and Molecular Biology, Inc.
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