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Microbiology and Molecular Biology Reviews, December 2004, p. 639-668, Vol. 68, No. 4
1092-2172/04/$08.00+0     DOI: 10.1128/MMBR.68.4.639-668.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.

Control of rRNA Synthesis in Escherichia coli: a Systems Biology Approach

Division of Molecular and Cellular Biosciences, National Science Foundation, Arlington, Virginia,¹ Department of Cell and Molecular Biology, BMC, Uppsala University, Uppsala, Sweden,² Department of Molecular and Cell Biology, University of Texas at Dallas, Richardson, Texas³

The first part of this review contains an overview of the various contributions and models relating to the control of rRNA synthesis reported over the last 45 years. The second part describes a systems biology approach to identify the factors and effectors that control the interactions between RNA polymerase and rRNA (rrn) promoters of Escherichia coli bacteria during exponential growth in different media. This analysis is based on measurements of absolute rrn promoter activities as transcripts per minute per promoter in bacterial strains either deficient or proficient in the synthesis of the factor Fis and/or the effector ppGpp. These absolute promoter activities are evaluated in terms of rrn promoter strength (V_max/K_m) and free RNA polymerase concentrations. Three major conclusions emerge from this evaluation. First, the rrn promoters are not saturated with RNA polymerase. As a consequence, changes in the concentration of free RNA polymerase contribute to changes in rrn promoter activities. Second, rrn P2 promoter strength is not specifically regulated during exponential growth at different rates; its activity changes only when the concentration of free RNA polymerase changes. Third, the effector ppGpp reduces the strength of the rrn P1 promoter both directly and indirectly by reducing synthesis of the stimulating factor Fis. This control of rrn P1 promoter strength forms part of a larger feedback loop that adjusts the synthesis of ribosomes to the availability of amino acids via amino acid-dependent control of ppGpp accumulation.

We dedicate this review in gratitude to Gunther S. Stent, who set the field about the control of ribosome synthesis and growth of bacteria in motion 45 years ago, when he and Sidney Brenner initiated the study of a mutant with an unusual response of RNA synthesis to amino acid starvation. Without his initial stimulus and the experience gained by trainees in the Stent laboratory, this review would not have been possible.

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